some in no particular order:

Sin/Braska's Final Aeon(Final Fantasy X)
Sephiroth(my personal favorite)(Final Fantasy VII)
Ganon(the N64 version, most of the other versions stink)
Psycho Mantis(Metal gear Solid)
The Collosi
Kefka (if this one is not in the top 10, your list sucks)
Bowser(the first time you ever fight him)
Darth Malak(KOTOR)
The Judges(Final Fantasy XII)
Through the Fire and Flames(Guitar Hero III)

Some good stuff there. Especially Psycho Mantis. Here are a few more.

Bowser (Paper Mario) - Paper Mario has the most epic Bowser fight in his long career of abduction.

The Black Knight (Fire Emblem) - Invincible armor, eh? Excuse me while I cower over here.

Ridley (Metroid Everything) - The space dragon which won't ever die. Jeebus.

Mike Tyson (Punch Out!!) - You felt like a champion just for getting to him, because you know you could never get past him.

GladOS (Portal) - It was the highlight of an incredibly good game. Why hasn't she been mentioned yet?

Balor (Myth: The Fallen Lords) - To defeat him, you have to cut off his head. To kill him, you have to toss his head into a bottomless pit before his lieutenant (who has cut off his face and his own heart in a black magic ritual and can transform into a murder of crows) hunts you down.

Letz Shake (No More Heroes) - Best powerup sequence in any video game ever.

I just drew this a while ago, Mr.Shine and Mr.Bright:

Pretty much one of my favorite bosses of all time, You have to admit, fighting the sun and moon is pretty cool ;)

The final fight in X was really easy (it may have been helped by the fact that Tidus could do 30,000 damage, but I compensated for that by not using tri of 9,999 + blitz ace = boss dead)

Anyway, here are the ones I can think of:

Colossus in God of War II, the King Bolan fight, Resistance battle against a stalker (something like that), the first assassination in Assassin's Creed, any of the epic ace combat battles against the stupid flying castles, GTA IV: the final boss on revenge, San Andreas ... I cant really think of many because I dont really like boss fights

the End MGS

Yeah MGS and FF Bosses FTW :D

I don't have an order, but...

Bowser from Paper Mario
Xehanort from Kingdom Hearts 2
Cackletta from Mario and Luigi
... can't think of more right now...

They were hard in Kirby's Adventure... I couldn't beat them for days

that's some pretty good artwork.. :D

That was the most mad I have been mad at a game....At least I got pay back with the real ending...