Final Answers

Alright, here is the list (which is of everything that I know that has appeared in a desert and desert ruins/caves, I don't count castles):

Enemies (mostly):
Pokey
Cobrat
Shy Guy
Bandit
Tweester
Piranha Plant
Venus Fire Trap
Koopa Troopa
Koopa Paratroopa
Goomba
Boomerang Bro.
Fire Bro.
Hammer Bro.
Buzzy Beetle
Spiny
Rappy, Armadillo, Scorpion, Mummy, Lilly, Skull, Pharoah Head (all from Donkey Kong GB)
Fireballs (two variants... I think)
Mini Shy Guy
Snifit
Bandit
Chain Chomp
Fire Snake
Dry Bones
Stone Chomp
Swooper
Mummy Pokey
Klepto
Toxbox
Lakitu
Spiny
Amp
Bob-omb
Grindel
Spindel
Fly Guy
Fire Chomp
Kuromame
Shrooba Diver
Dark Boo
Elite Boom Guy
Snifaro
Monty Mole
Gritty Goomba
Spiky Snifit
Birdo (Pink Birdo, Red Birdo, Green Birdo)
Anuboo
Red Chomp
Bullet Bill
Kamek
Spike Bass
Blockhopper
Spike
Crabbers
Cluckboom
Panser
Magikoopa
Boo
Mines
Water Shooters
Albatoss
Beezo
Hoopster
Ninji
Spiky Plants
Pokey Sprout
Rhomp
Firebars
Silver Chomp
Sledge Bros.
Fuzzies
Angry Sun
Pile Driver Micro-Goomba
Cheep Cheep
Super/Cactus Piranha Plant (MKDD Dry Dry Desert Course)
Bald Cleft
Boomboxer
Cherbil
Ice Cherbil
Jawbus
Megabite
Spiked Goomba
Squig
Squiglet
Spiky Tromp
Frackle
Bombshell Koopa
Bunbun
Fly (Super Mario Land)
Gao
Thwomp
Cleft
Sandmaargh
Tail Thwomp
Tail Goomba
Wallop
Blokkablok
Limbo Bro.

Bosses:
Fracktail
O'Chunks
Squizzard
Tryclyde
Trunkle
Tutankoopa
King Tut
Petey Piranha
Mummipokey
King Totomesu
Buzzar

NPCs:
Dryites
Moustafa
Mr. E (Paper Mario)
Nomadimice
Toads
Hootenanny
Steamer

This might as well be our final answer.
Can't get much more, and I'm not sure if there is penalty for anything that might not be considered legitimate.
 
Alright, I'm not sure how legal this is, but:

Characters:
Waluigi - Mario Tennis
Wanda - Mario & Wario
Wandering Nomadimouse - Paper Mario
Walter - Super Paper Mario
Wario - Super Mario Land 2: 6 Golden Coins
Wario-Man - WarioWare: Twisted!
Wart - Yume Kōjō: Doki Doki Panic/Super Mario Bros. 2
Watinga - Mario Paint
Watt - Paper Mario
Webber - Wario Land 3
Welderberg - Super Paper Mario
Wendy O. Koopa - Super Mario Bros. 3
Whacka - Paper Mario
Whale - Paper Mario
Whibbi - Super Paper Mario
Whittle - Super Mario Galaxy 2
Whisker - Mario Tennis: Power Tour
Whispy Woods - Super Smash Bros.
White Mage - Mario Hoops 3-on-3
White Shy Guy - Yoshi's Story
Whomp King - Super Mario 64
Wiggler - Super Mario Sunshine
Wiggler Family - Mario & Luigi: Bowser's Inside Story
Willy - Mario Tennis: Power Tour
Wings of Night - Paper Mario: The Thousand-Year Door
Winkle - Mario & Luigi: Superstar Saga
Winnie - Super Paper Mario
Winter Windster - Wario World
Wisdurm - Mario & Luigi: Bowser's Inside Story
Wise Wisterwood - Paper Mario
Wizenheimer - Super Mario World
Wizard King of the West - The Adventures of Super Mario Bros. 3
Wolf O'Donnell - Super Smash Bros. Brawl
Wolfenboss - Wario Land 3
Wonky - Paper Mario: The Thousand-Year Door
Woody - Mario Party 2
Wooster - Nintendo Comics System
Wormwould - Wario Land 3

Places:
Waffle Kingdom – Paper Mario: The Thousand-Year Door
Waluigi Pinball – Mario Kart DS
Waluigi Pinball – Mario Sports Mix
Waluigi Room – Mario Party 4
Waluigi Stadium – Mario Kart: Double Dash!!
Waluigi's Island – Mario Party 3
Wardrobe Room – Luigi's Mansion
Wario Colosseum – Mario Kart: Double Dash!!
Wario Factory – Mario Hoops 3-on-3
Wario Factory Court – Mario Power Tennis
Wario Field – Super Mario Stadium Baseball
Wario Palace – Mario Superstar Baseball
Wario Room – Mario Party 4
Wario Stadium – Mario Kart 64
Wario's Battle Canyon – Mario Party
Wario's Carnival – Dance Dance Revolution: Mario Mix
Wario's Castle – Super Mario Land 2: 6 Golden Coins
Wario's Gold Mine – Mario Kart Wii
Wario's Woods (place) – Wario's Woods
WarioWare, Inc. (company) – WarioWare, Inc.: Mega Microgame$!
WarioWare (stage) – Super Smash Bros. Brawl
Warp Zone – Super Mario Bros.
Washroom (1F) – Luigi's Mansion
Washroom (2F) – Luigi's Mansion
Wavy Beach – Super Princess Peach
Way Cool – Super Mario World
Wendy's Blitz Snarlton Hotel – Hotel Mario
Western Land – Mario Party 2
Westside Goods – Paper Mario: The Thousand-Year Door
Wet-Dry World – Super Mario 64
Whoa Zone – Super Paper Mario
Whomp's Fortress – Super Mario 64
Wiggler's Garden – Mario Party DS
Wild Glide Galaxy – Super Mario Galaxy 2
Wild Ride in the Sky – Super Mario Advance 4: Super Mario Bros. 3
Windmillville – Mario Party 7
Windy Mill – Paper Mario
Winged Mario Over the Rainbow – Super Mario 64
Winkle Colosseum – Mario & Luigi: Superstar Saga
Woody Woods – Mario Party 3
Woohoo Hooniversity – Mario & Luigi: Superstar Saga
World 0 – Super Mario World 2: Yoshi's Island
World 1 (Mario & Wario) – Mario & Wario
World 1 (New Super Mario Bros.) – New Super Mario Bros.
World 1 (New Super Mario Bros. Wii) – New Super Mario Bros. Wii
World 1 (Super Mario Bros.) – Super Mario Bros.
World 1 (Super Mario Bros.: The Lost Levels) – Super Mario Bros.: The Lost Levels
World 1 (Super Mario Bros. 2) – Super Mario Bros. 2
World 1 (Super Mario Galaxy 2) – Super Mario Galaxy 2
World 1 (Super Mario World 2: Yoshi's Island) – Super Mario World 2: Yoshi's Island
World 1 (Yoshi's Island DS) – Yoshi's Island DS
World 1 (Super Mario 3D Land) – Super Mario 3D Land
World 1 (New Super Mario Bros. 2) – New Super Mario Bros. 2
World 2 (Mario & Wario) – Mario & Wario
World 2 (New Super Mario Bros.) – New Super Mario Bros.
World 2 (New Super Mario Bros. Wii) – New Super Mario Bros. Wii
World 2 (Super Mario Bros.) – Super Mario Bros.
World 2 (Super Mario Bros.: The Lost Levels) – Super Mario Bros.: The Lost Levels
World 2 (Super Mario Bros. 2) – Super Mario Bros. 2
World 2 (Super Mario Galaxy 2) – Super Mario Galaxy 2
World 2 (Super Mario World 2: Yoshi's Island) – Super Mario World 2: Yoshi's Island
World 2 (Yoshi's Island DS) – Yoshi's Island DS
World 2 (Super Mario 3D Land) – Super Mario 3D Land
World 2 (New Super Mario Bros. 2) – New Super Mario Bros. 2
World 3 (New Super Mario Bros.) – New Super Mario Bros.
World 3 (New Super Mario Bros. Wii) – New Super Mario Bros. Wii
World 3 (Super Mario Bros.) – Super Mario Bros.
World 3 (Super Mario Bros.: The Lost Levels) – Super Mario Bros.: The Lost Levels
World 3 (Super Mario Bros. 2) – Super Mario Bros. 2
World 3 (Super Mario Galaxy 2) – Super Mario Galaxy 2
World 3 (Super Mario World 2: Yoshi's Island) – Super Mario World 2: Yoshi's Island
World 3 (Yoshi's Island DS) – Yoshi's Island DS
World 3 (Super Mario 3D Land) – Super Mario 3D Land
World 3 (New Super Mario Bros. 2) – New Super Mario Bros. 2
World 4 (New Super Mario Bros.) – New Super Mario Bros.
World 4 (New Super Mario Bros. Wii) – New Super Mario Bros. Wii
World 4 (Super Mario Bros.) – Super Mario Bros.
World 4 (Super Mario Bros.: The Lost Levels) – Super Mario Bros.: The Lost Levels
World 4 (Super Mario Bros. 2) – Super Mario Bros. 2
World 4 (Super Mario Galaxy 2) – Super Mario Galaxy 2
World 4 (Super Mario World 2: Yoshi's Island) – Super Mario World 2: Yoshi's Island
World 4 (Yoshi's Island DS) – Yoshi's Island DS
World 4 (Super Mario 3D Land) – Super Mario 3D Land
World 4 (New Super Mario Bros. 2) – New Super Mario Bros. 2
World 5 (New Super Mario Bros.) – New Super Mario Bros.
World 5 (New Super Mario Bros. Wii) – New Super Mario Bros. Wii
World 5 (Super Mario Bros.) – Super Mario Bros.
World 5 (Super Mario Bros.: The Lost Levels) – Super Mario Bros.: The Lost Levels
World 5 (Super Mario Bros. 2) – Super Mario Bros. 2
World 5 (Super Mario Galaxy 2) – Super Mario Galaxy 2
World 5 (Super Mario World 2: Yoshi's Island) – Super Mario World 2: Yoshi's Island
World 5 (Yoshi's Island DS) – Yoshi's Island DS
World 5 (Super Mario 3D Land) – Super Mario 3D Land
World 5 (New Super Mario Bros. 2) – New Super Mario Bros. 2
World 6 (New Super Mario Bros.) – New Super Mario Bros.
World 6 (New Super Mario Bros. Wii) – New Super Mario Bros. Wii
World 6 (Super Mario Bros.) – Super Mario Bros.
World 6 (Super Mario Bros.: The Lost Levels) – Super Mario Bros.: The Lost Levels
World 6 (Super Mario Bros. 2) – Super Mario Bros. 2
World 6 (Super Mario Galaxy 2) – Super Mario Galaxy 2
World 6 (Super Mario World 2: Yoshi's Island) – Super Mario World 2: Yoshi's Island
World 6 (Super Mario 3D Land) – Super Mario 3D Land
World 6 (New Super Mario Bros. 2) – New Super Mario Bros. 2
World 7 (New Super Mario Bros.) – New Super Mario Bros.
World 7 (New Super Mario Bros. Wii) – New Super Mario Bros. Wii
World 7 (Super Mario Bros.) – Super Mario Bros.
World 7 (Super Mario Bros.: The Lost Levels) – Super Mario Bros.: The Lost Levels
World 7 (Super Mario Bros. 2) – Super Mario Bros. 2
World 7 (Super Mario 3D Land) – Super Mario 3D Land
World 8 (New Super Mario Bros.) – New Super Mario Bros.
World 8 (New Super Mario Bros. Wii) – New Super Mario Bros. Wii
World 8 (Super Mario Bros.) – Super Mario Bros.
World 8 (Super Mario Bros.: The Lost Levels) – Super Mario Bros.: The Lost Levels
World 8 (Super Mario 3D Land) – Super Mario 3D Land
World 9 (New Super Mario Bros. Wii) – New Super Mario Bros. Wii
World 9 (Super Mario Bros.: The Lost Levels) – Super Mario Bros.: The Lost Levels
World A – Super Mario Bros.: The Lost Levels
World B – Super Mario Bros.: The Lost Levels
World C – Super Mario Bros.: The Lost Levels
World D – Super Mario Bros.: The Lost Levels
World-e – Super Mario Advance 4: Super Mario Bros. 3
World S – Super Mario Galaxy 2
World Mushroom (New Super Mario Bros. 2) – New Super Mario Bros. 2
World Flower (New Super Mario Bros. 2) – New Super Mario Bros. 2
World Star (New Super Mario Bros. 2) – New Super Mario Bros. 2
World of Nothing – Super Paper Mario
Wreck Train – Wario Land: Shake It!

Enemies:

Waiter – Luigi's Mansion
Walking Flame – Donkey Kong (Game Boy)
Wall Lakitu – Super Mario World 2: Yoshi's Island
Wallop – Super Mario 3D Land
Walrus – Donkey Kong (Game Boy)
Walruss – Super Princess Peach
Waluigi – Mario Tennis
Wanderin' Goom – Wario Land: Super Mario Land 3
Warpid – Super Paper Mario
Wario – Super Mario Land 2: 6 Golden Coins
Wario Mask – Super Mario Land 2: 6 Golden Coins
Watch – Wario Land: Super Mario Land 3
Water Hand – Wario Land 3
Water Spark – Wario Land 3
Webber – Wario Land 3
Wendy O. Koopa – Super Mario Bros. 3
Wereturtle – The Super Mario Bros. Super Show!
Whale – Super Mario Bros. 2
Whirly Fly Guy – Super Mario World 2: Yoshi's Island
White Clubba – Paper Mario
White Magikoopa – Paper Mario
White Puff – Wario Land: Super Mario Land 3
Whimp – Super Mario Galaxy 2
Whomp – Super Mario 64
Wiggler – Super Mario World
Wild Ptooie Piranha – Super Mario World 2: Yoshi's Island
Wind Duppy – Super Mario Sunshine
Wind Winder – Wario World
Windbag – Yoshi's Island DS
Winged Anvil – Winged Anvil
Witch – Wario World
Wisdurm – Mario & Luigi: Bowser's Inside Story
Wizard (Wario Land II) – Wario Land II
Wizenheimer – Super Mario World (television series)
Wizzerd – Paper Mario: The Thousand-Year Door
Wonder Thwack – Mario & Luigi: Partners in Time
Woozy Guy – Yoshi's Island DS
Wrackle – Super Paper Mario

Items:
Wacky Watch – Mario Party 3
Wake Up Pin – Super Mario RPG: Legend of the Seven Stars
Wallet – Super Mario RPG: Legend of the Seven Stars
Waluigi Racer – Mario Kart: Double Dash
War Fan – Super Mario RPG: Legend of the Seven Stars
Warehouse Key – Paper Mario
Warm Cocoa – Super Paper Mario
Wario Bike – WarioWare, Inc.: Mega Microgame$!
Wario Car – Mario Kart: Double Dash
Wario Key – Super Mario 64 DS
Wario's Cap – Super Mario 64 DS
Wario's Hat – Super Mario Land 2: 6 Golden Coins
Wario's Laptop – WarioWare, Inc.: Mega Microgame$!
Wario's Treasures – Wario Land series
Warp Block – Mario Party 2
Warp Dice Block – Mario Party DS
Warp Pipe – Super Mario Bros.
Warp Whistle – Super Mario Bros. 3
Waste Basket – Super Mario RPG: Legend of the Seven Stars
Water Barrel – Super Mario Sunshine
Water Bottle – Super Mario Sunshine
Water Rocket – Super Mario Sunshine
Water Shooter – Super Mario Galaxy
Water Stone – Paper Mario
Watermelon – Yoshi's Story
Wedding Ring – Paper Mario: The Thousand-Year Door
Weight – Paper Mario
Weird Extract – Super Paper Mario
Weird Mushroom – Super Mario RPG: Legend of the Seven Stars
Whacka Bump – Paper Mario
Whiskered Eggplant – Mario Superstar Baseball
White-Green Checkered Block – New Super Mario Bros. Wii
Whomp Glove – Super Mario RPG: Legend of the Seven Stars
Wicked Weather Satellite – The Super Mario Bros. Super Show!
Wildlife – Mario Kart DS
Wilt Shroom – Super Mario RPG: Legend of the Seven Stars
Wing Cap – Super Mario 64
Winged Cloud – Super Mario World 2: Yoshi's Island
Winkle Card – Mario & Luigi: Superstar Saga
Wishstone – Wario: Master of Disguise
Wooden Chest – Wario World
Wooden Trapdoor – Wario World
Work Pants – Super Mario RPG: Legend of the Seven Stars
Wrestling Mag – Paper Mario: The Thousand-Year Door
 
Alright, I guess here's our list.

1-Up Mushroom · 1-Up Super · Absorbing Mushroom · Amanita · Bad Mushroom · Bee Mushroom · Berry Mushroom · Boo Mushroom · Cursed Mushroom · Dried Shroom · Ghost Shroom · Ghoul Shroom · Golden Mushroom · Invincishroom · Life Shroom · Life Mushroom · Long-Last Shake · Max Mushroom · Mega Mushroom · Metal Mushroom · Mid Mushroom · Mini Mushroom · Moldy Mush · Mushroom · Mushroom Drop · Poison 1-Up · Poison Mushroom · Propeller Mushroom · Refreshroom · Reverse Mushroom · Rock Mushroom · Rotten Mush · Shroob Mushroom · Slimy Shroom · Slow Shroom · Sluggish Shroom · Spring Mushroom · Super Acorn · Super Mega Mushroom · Super Mini Mushroom · Super Mushroom · Super Shroom · Ultra Shroom · Shroom Shake · Super Shroom Shake · Ultra Shroom Shake · Vacuum Shroom · Volt Shroom · Weird Mushroom · Wilt Shroom · Zombie Shroom· Fried Shroom · Fried Shroom Plate · Fruity Shroom · Honey Shroom · Honey Super · Honey Ultra ·  Hot Shroom · Jelly Shroom · Jelly Super · Jelly Ultra · Maple Shroom · Maple Super · Maple Ultra · Shroom Cake · Shroom Steak · Volcano Shroom · Sweet Shroom · Mushroom Platform (Orange) · Mushroom Platform (Red) · Mushroom Platform (Green) · Mushroom Platform (Trampoline) · Mushroom Platform (Sinking - Blue) · Mushroom Platform (Rising - Red)

I'm not sure if we can count every variant for the mushroom platforms as legal. Especially ones that are just minor color swaps. The ones listed are ones that are unique in various games (orange can be the square ones from SM3DL, red can be the bouncy ones from Mushroom Gorge, with the green ones being from the same area, and the trampoline one being the ones that constantly force you to bounce from one of the main Mario games, I think NSMB, and the sinking and rising ones, which do so when you are on them, from NSMB2).
 
Blizzard-Super Mario World 2:Yoshi's Island
Chilly Waters-Mario Party 3
Christmas Village-Mario and Sonic at the Olympic Winter Games
Chief Chilly Challenge-Super Mario 64 DS
Cool,Cool Mountain-Super Mario 64
DK Pass-Mario Kart DS
Fahr Outpost-Paper Mario The Thousand Year Door
Frappe Snowland-Mario Kart DS
Freeze Mountain-Dance Dance Revolution:Mario Mix
Freezeflame Galxey-Super Mario Galxey
Freeze Flake Galxey-Super Mario Galxey 2
Frostown-Mario and Sonic at the Olympic Winter Games
Frosty Fronteir-Mario Pinball Land
Geleam Glacier-Super Princess Peach
Ice Game Room-Mario Party Advance
Ice Stadium-Mario Party Advance
Iced Land-Super Mario Bros.3
Iceberg-Donkey Kong GBA
Icepark-Mario and Sonic at the Olympic Winter Games
Joke's End-Mario and Luigi Superstar Saga
Mt.Frostbit-Super Mario Galxey
Peach Ice Garden-Mario Super Sluggers
Polastraits-Mario and Sonic at the Olympic Winter Games
Rosalina's Ice World-Mario Kart 7
Sherbet Land {Wario Land}-Wario Land:Super Mario Land:3
Sherbet Land{Course}-Mario Kart 64
Shiver City-Paper Mario
Shivering Mountains-Wario World
Shiver Mountain-Paper Mario
Shiver Region-Paper Mario
Shiver Snowfield-Paper Mario
Siverburn Galxey-Super Mario Galxey 2
Snow Area-Mario Party Advance
Snow Cup Galxey-Super Mario Galxey
Snow Land-Mario Kart Super Circuit
Snow Panic-Mario Kart Arcade GP
Snowflake Lake-Mario Party 6
Snowman's Land-Super Mario 64
Sparkleton-Mario and Sonic at the Olympic Winter Games
 
Volcano Spreading Flames-Mario Party 1
Boswer Parade-Mario Party 2
Crumbling Bridges-Mario Party 4
Extra Start-Mario Party 4
Loto Shop-Mario Party 4
Capsule Machines-Mario Party 5
Chain Chomps-Mario Party 6
Mecha-Bowser-Mario Party 7
Roller coaster-Mario Party 7
Can't buy stars-Mario Party 8
Jackpot Machine-Mario-Party 9
No actual hazards-Mario Party 9
Slot Machine-Mario Party DS
 
Albatoss-Super Mario Bros. 2
Autobomb-Super Mario Bros. 2
Beezo-Super Mario Bros. 2
Cobrat-Super Mario Bros. 2
Flurry-Super Mario Bros. 2
Hoopster-Super Mario Bros. 2
Ninji-Super Mario Bros. 2
Ostros-Super Mario Bros. 2
Pansers-Super Mario Bros. 2
Phanto-Super Mario Bros. 2
Pidgit-Super Mario Bros. 2
Porcupo-Super Mario Bros. 2
Shy Guy-Super Mario Bros. 2
Snifit- Super Mario Bros. 2
Spark-Super Mario Bros. 2
Trouter-Super Mario Bros. 2
Tweeter-Super Mario Bros. 2
Whale-Super Mario Bros. 2
Birdo-Super Mario Bros. 2
Mouser-Super Mario Bros. 2
Red Birdo-Super Mario Bros. 2
Tryclyde-Super Mario Bros. 2
Fryguy-Super Mario Bros. 2
Mini Fryguy-Super Mario Bros. 2
Gray Birdo-Super Mario Bros. 2
Clawgrip-Super Mario Bros. 2
Green Birdo-Super Mario Bros. 2
Wart-Super Mario Bros. 2
Pile Driver Micro-Goombas-Super Mario Bros. 3
Red Paragoomba-Super Mario Bros. 3
Shoe Goomba-Super Mario Bros. 3
Colossal Koopa Paratroopa-Super Mario Bros. 3
Buster Bettle-Super Mario Bros. 3
Nipper Plant-Super Mario Bros. 3
Piranhacus Gigantic-Super Mario Bros. 3
Hot Foot-Super Mario Bros. 3
Roto Disc-Super Mario Bros. 3
Stretch-Super Mario Bros. 3
Big Bertha-Super Mario Bros. 3
Baby Cheeps-Super Mario Bros. 3
Jelectros-Super Mario Bros. 3
Lava Lotus-Super Mario Bros. 3
Angry Sun-Super Mario Bros. 3
The Big Boo{boss}-Super Mario World
Amazing Flyin' Hammer-Super Mario World
Beach Koopa-Super Mario World
Big Blue Boo-Super Mario World
Big Steely-Super Mario World
Blargg-Super Mario World
Blurp-Super Mario World
Boo Buddy Block-Super Mario World
Boo Buddy Snake-Super Mario World
Boo Buddy Swarm-Super Mario World
Chargin' Chuck-Super Mario World
Circling Boo Buddies-Super Mario World
Climbing Koopa-Super Mario World
Dino Rhino-Super Mario World
Dino Torch-Super Mario World
Disappearing Boo Buddies-Super Mario World
Eerie-Super Mario World
Fishing Boo-Super Mario World
Fishing Lakitu-Super Mario World
Floating Mine-Super Mario World
Flying Goomba-Super Mario World
Grinder-Super Mario World
Hothead-Super Mario World
Jumping Piranha Plant-Super Mario World
Kamikaze Koopa-Super Mario World
Li'l Sparky-Super Mario World
Mega Mole-Super Mario World
Muncher-Super Mario World
Break Pillars-Super Mario Word
Pipe Lakitus=Super Mario World
Rex-Super Mario World
Rip Van Fish-Super Mario World
Skull Box-Super Mario World
Sumo Bro-Super Mario World
Super Koopa-Super Mario World
Volcano Lotus-Super Mario World


 
The Legend of Zelda: A Link to the Past-Mario's face can be seen as framed photos in many houses.
The Legend of Zelda: Link's Awakening-There are many Mario-related enemies in the game, along with a Yoshi Doll as an item.
The Legend of Zelda: Ocarina of Time- There are framed pictures of Mario,Luigi,Peach and Bowser in the Hyrule Castle.
-Also in Lon-Lon Ranch, all the people have Bowser medals on their necks.
The Legend of Zelda:  Majora's Mask-One of the masks that the Masks Salesman has is a face of Mario.
The Legend of Zelda: Twilight Princess- Fyer, the man who operates the cannon, has a Bullet Bill on his arm.
Animal Crossing-There is a Mario and Lugi statue
-There is also code only Super Mario Bros. related furniture
-The game also has the Classic Super Mario Bros.games for the Nintendo Entertainment System
-There is also two shirts with Mario and Luigi logos on them.
Animal Crossing Wild World-Super Mario Bros furniture can be received by Nintendo Wi-Fi Connection letters to Nintendo
-Additionally, Super Mario Bros. 3 paper is in the game
Animal Crossing: City Flolk-Furniture from Mario can sometimes be found in floating presents
-Also Mario and Luigi costumes can be bought at Mable and Able's store
Kirby Super Star when fighting in a ring,you will see Mario,Luigi,Birdo and Toad cheering you on
Kirby Super Star Ultra-Mario,Luigi,Peach,Wario and Two Toads are in the audience
Pikmin 2-One of the items is a bottle cap with Bowser
-One of the says Mario Paint on it
-One of the items is Princess Peach's crown
Brain Age-If you touch the man that is at walking  speed,he will whistle the Mario theme
Call of Duty: Modern Warfare 2-Price a charcter form the series is in the form of a Super Mario Bros. sprite
Picross DS-After completing all the normal mode puzzles, ten Mario themed puzzles can be unlocked
Sonic the Hedgehog-In Marble Zone, a pattern on a temple in the background resembles Mario's face
Mike Tyson's Punch out-Mario is the referee
Tennis NES-mario was the referee
 
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