Rundas in Metroid Prime 3: Corruption: Corruption had a lot of good fights, but the Rundas one stands out. This is mostly due to the soundtrack, but it was still a tense, hectic fight throughout that was really enjoyable to play.
Sword and Axe from Prince of Persia: The Two Thrones: By Warrior Within, the The Sands of Time trilogy had a lot of truly memorable bosses. Sword and Axe were among the best. This is mostly because it actually mixes up the "arena" fights from the two games by giving you two guys to go against in a more free-moving, fast fight. Granted, the "strike one until the other attacks" isn't really unique, but it was still a lot of fun.
The Vizier from Prince of Persia: The Two Thrones: This may have been more memorable simply for being the last boss in the trilogy (well, there is the level with The Dark Prince, but that's not really a fight). Still, I thought it did a very good job of mixing the platforming of the series into the boss, and unlike the first boss of the game, they actually did a good job with the whole fight.
Argorok from The Legend of Zelda: Twilight Princess: The atmosphere, though unoriginal, was fantastic for the fight. It also was a lot of fun to just grapple around the arena. Part of me wishes that it had lasted longer, but what we got was one of the most exciting bosses I've faced.