One of my favorite fianl boss fights was on Twilight Princess. They had you do so much to defeat him. I love battling bosses that have many forms to them because it just makes the games more interesting.
The Finalhazard on Sonic Adventure 2(it was epic) and the ending chapter; Repatriation on Fire Emblem(9): Path of Radiance where Ashnard; the King of Daein is the final boss.