Naxx was before my time, and I’m still in T5 (just downed Leo); the most annoying boss fight I’ve encountered is Blackheart the Inciter in SL (assuming you don’t outgear the place). “Time for fun!” “Fuck! There go my cooldowns.”
A’lar was a huge pain in the ass (I’m a fire mage) but we got him.
Yeah, that one sucked. I reloaded too many times to count and finally managed to get the thing. For the most part the frog hunt was fun. Admittedly, I used a FAQ for the frog locations, just because I was also going for a no kill (well, okay limited kill, since the bosses die whether or not you actually kill them or knock them out), and searching high and low for hidden frogs while my enemies aren’t dead would have been an excercise in annoyance. (Much like tagging the aforementioned frog on the runway was.)
The really nice part about the no-kill though:
I must say, though, no kill dramatically speeds up the game when the dream river scene comes. I heard about one guy who killed all enemies up to that point and had to wade through hundreds of ghosts. With no-kill, the only ghosts you encounter are the bosses.
The speed problem happened to me with that game even just in the lead up to the final boss - the Mûmakil had a move which stunned and forced you back down the action track, so they’d spam their more damaging moves, stun, then back to the damaging again. Probably the first time I felt what it must be like when I abuse stunlocking in games on enemies. 
I wasn’t all that impressed with the final boss (and the one before it) and Assassin’s Creed. Here we are, being Mr. Sneaky, and the game throws a long enemy battle gauntlet at you.
Good boss fights; well, Shadow of the Colossus, and pretty much all of them, though my favourite has to be Avion.
Oh yeah. That’s why I said “second playthrough” - the first time, when I was totally unprepared, was a bitch. All of the monsters were cheaty like that. It’s no fun if you’re yelling at the screen in frustration. 
And here I had thought no one else had played that game.
My favorite boss fight was Kingdom Hearts. Can’t remember the name of the boss, but I loved that game.
And Contra from the old NES days. Don’t remember anything about it except the damn cheat code
up, up, down, down, left, right, left, right, b, a, b, a, start…
whew…
YES! Infinate lives and ammo!
If we’re talking about WoW bosses, then I have to bring up Teron Gorefiend. The fight is that you basically get to sit there and do as much damage as possible, until he puts a curse on you that turns you into a ghost. You can no longer damage anything except these three other ghosts that appear around you. You have to kill them before they get to the rest of the players lest they start slaughtering you. Also, you can’t use any of your usual abilities, they get replaced with others.
I’ve fought him probably around 40 times killed him probably three of those times. Such a pain in the ass. Of course, it’s not official until the GM yells over Vent, “Who failed and let their constructs in the raid? Why did you fail? I could do it. It’s not that hard. You just suck.”
Of course, my last GM was a real fuckface.
I think judging by sales figures and reviews having sold just two copies of the game wouldn’t be all that surprising. I certainly wouldn’t have recommended it (though I did replay it. I presume i’m just insane).
I’ve thought of another; Neverwinter Nights 2. Let alone the terrible ending afterwards, you get given a fantastic super-longsword, which is just great should you be playing, say, a bow-specced ranger, or indeed have any feats for weapons other than longsword which are now useless.
Though you didn’t need the longsword in that fight. You could use its abilities without it being equipped and you could destroy the portal just fine without it. Heck first playthrough I had a monk beat the portal to death with his fists.
True, but just felt annoyed that they’d given me this fantastic weapon, one which is pretty much fantastic whether or not you’ve been feating towards it (unless you actually can’t equip the thing), which negates pretty much anything else you’ve built your character as, and may actually be better.
Nitpick: Last time I checked, that sword is listed as a “universal sword” and doesn’t get the benefit of any feats at all. Which is really annoying if you took the Weapon Master prestige class, doubly so if your weapon of choice is longsword (though you really should pick either scythe or falchion).
Ah, I suppose that’s to get around the “can’t equp” issue.
I’ve only been to Naxx once, the whole group was level 70, and walk in the park me gnomish bottom. Pity we never got 'round to going back there. Can’t wait to see the revamped version.
I think SL may be the best-designed instance in the game. I don’t like 25-man raids, as either you take them “Marine style” going hop, hop, hop focus, focus, focus, bang bang bang (which ends up giving me a crick on my neck) or you manage to spend over one hour just waiting for people to get together (I’m often the first person at the instance, maybe I should work on being less punctual). 5-10 man work well for me. SL does not favor any tanking style/class over others, nor a kind of healer; Blackheart is definitely in the list of 3-most-hated bosses, judging by how people moan about him; the third guy can be kick-bang-dead or manage to kill a group so many times they give up; the alley leading to Murmur requires finesse to pull at the right times; Murmur requires people to be alert to their own attacks, their own debuffs and their neighbors’ debuffs at the same time, yet there have been times we’ve managed to kill his gassy bum after he’d fried the healer in the first minute (don’t ask me why she was that close).
None of those bosses is, in and on itself, as megasuperspectacular as some others, but the whole instance is very, very well done.
For some reason Blackheart likes to make my mage use her sword. That may be artificial but it sure isn’t intelligent 