Ganon from OoT is the greatest. Ganondorf suddenly emerges from the collapsed castle, and then he transforms into a massive beast! Then you lose your sword and engage in a desperate battle (Provided you don't use the Biggoron Sword). Throughout the battle, a dreary music plays, and Ganon is nearly impossible to see except when the lightning flashes. The tension is built to massive heights as you battle inside a ring of flame. Then at last you defeat Ganon and stab him in the face! Then you at last exhale as you realize it's all over. You realize you've been sweating with excitement at one of the best boss battle's ever.
My favorite boss, final or not, is Majora. Not only is the sense of atmosphere heavy in the fight, but it's also a fun and challenging 3 phase fight! ...Assuming you don't cheap out and use the Fierce Diety's Mask.
Favorite final boss was Ganon from OoT. That fight was just so epic. I was maybe 6 or 7 years and I though I really defeated Ganondorf and finished the game. Then Ganondorf emerged from the ruins and transformed in the ultimate beast Ganon. Epic, just epic.