Good thread. Digging it up because I've been thinking about making one about good boss fights myself, but wanted to see when the last one was, if there was one at all.
Personally, I much prefer the boss fights where you're fighting an equal, a rival, a person, rather than a giant monster bug alien thing.
Recent games I think did a good job that didn't get enough credit for it were:
The last boss of Infamous. I found it fairly difficult, and pretty epic, both the location and the identity of the boss. His/Her attacks were equatable to my own, but different. I could see a main character in an Infamous game having this boss's abilities, which I think is a very strong quality in a game boss.
Bosses from Vanquish. Yeah, I'll find a chance to talk about Vanquish anywhere I can get. What makes Vanquish's bosses special to me is the way they're so smoothly woven into the battles it's almost hard to discern when an enemy is a boss and when it's just a strong enemy. The final battle is of particular note, in that again you're not shown a huge monster which then simply swings a big tentacle-limb at you every 7 seconds, and otherwise sits there and gets beat up upon. Unlike almost any game, the last boss in Vanquish is constantly dodging, evading, swooping, etc. There's hardly a "I just swung, so now I'll sit here for you to get in your five hits before I recover." You CAN stun this boss, but it's not a scripted mechanic for this one enemy; it fits into the overall fiction of the entire world, and is at the same time much harder to pull off here than perhaps anywhere else in the game. Mikami is a genius.
Darksiders: Not a single "dungeon" battle sticks out in my mind as being note-worthy, other than "hey, this is like Zelda." But the rival battles you have during the game all stick out in my head. It's so much more rewarding when a boss or enemy, really actually has some narrative to give it some meaning other than "big scary thing here to kill you." These enemies have motives, flaws, and strengths. Now, that said, the last boss is sort of a monster, kinda, which is why I'm saving Darksiders for last. I know that goes against everything else I've said, but it's like what Penny-Arcade said: it should be totally corny, a game called Darksiders, a sword named the "Chaos Eater," and all that adolescent nonsense. So should a monster boss. But, it all just works for Darksiders. I should totally think War is a corny, lame character, yet I think he's kinda bad-ass. Can't fully explain why Darksiders gets the pass from me and so many of us... maybe it's the accent?
Also worth noting is the Zant battle from Zelda: Twilight Princess. The combat in Zelda is really not very good, but that's not what makes the battle special. It's the environment, and how it changes, that sets this one apart. Really, I feel this was the game's high-note, at least as far as the conflicts went. The dungeon climax was much earlier.
