I can't really think of one. Despite being quite different from the boss fights mentioned here, the final four bosses of Fire Emblem Radiant Dawn are my favorite battles.
-Zelgius/The Black Knight: Despite being impossible to lose, the clip going into the fight, and the death sequence are very good. And the Black Knight has an epic battle theme.
-Dhegensia (or something like that...): HOLY CRAP I'M SCREWED!!! Nothing says that more than a large Black Dragon that can kill everyone you have in one or two shots, and is very hard to kill. The death sequence was also pretty good.
-Lehran/Sephiran: See Zelgius, but slightly harder, and without the clip leading to it.
-Ashera: This took forever. At the time, I was using Ike to attack at the start of every turn. Needless to say, it took a while to win this one. Also, it felt good to finally finish that game.
With more conventional boss fights, anything from Twilight Princess, Ocarina of Time, and the final few bosses in Four Sword adventure.
-Zelgius/The Black Knight: Despite being impossible to lose, the clip going into the fight, and the death sequence are very good. And the Black Knight has an epic battle theme.
-Dhegensia (or something like that...): HOLY CRAP I'M SCREWED!!! Nothing says that more than a large Black Dragon that can kill everyone you have in one or two shots, and is very hard to kill. The death sequence was also pretty good.
-Lehran/Sephiran: See Zelgius, but slightly harder, and without the clip leading to it.
-Ashera: This took forever. At the time, I was using Ike to attack at the start of every turn. Needless to say, it took a while to win this one. Also, it felt good to finally finish that game.
With more conventional boss fights, anything from Twilight Princess, Ocarina of Time, and the final few bosses in Four Sword adventure.