Most of the bosses from Twilight Princess, definitely! Particularly the water creature in the Water Temple, the aforementioned dragon in the Sky Temple, and the wicked awesome skeleton thing in the Arbiter's Grounds that you fight on that awesome floating disc (good god the name escapes me!). Twilight Princess is full of epic encounters!

I'll second the notion of the original Kingdom Hearts. I'm of the opinion that the series has gone way down hill since its brilliant debut, and the bosses are a huuuuuuuge part of the reason why. KH1 was a wonderfully challenging action/RPG, and nothing proved it better than its amazing bosses. The encounters with Riku, Malifecent Dragon, Darkside, Sephiroth, the Titans, and the final encounter with Ansem are all spectacular, though it must be said that nearly every fight in the game brings some great moments with it!

Shadow of the Colossus. Kind of obvious.

Every single boss fight and setpiece moment in Metal Gear Solid 4: Guns of the Patriots.

Most of the bosses in Shin Megami Tensei: Nocturne and the Digital Devil Saga games. It's exceedingly rare for an RPG to have genuinely involving boss fights, but these games succeed with style, creativity, challenge, and balance.

That's all I can think of for now! :P