Dahaka (Prince of Persia - Warrior Within) - Very difficult to beat on hard difficulty. I had to re-think my strategy million of times to beat him.
Kerrigan (Starcraft II - Wings of Liberty) - I used that device that allow you to control Zerg and I controlled tons of Broodlords to wipe out Kerrigan
General Gaius (Dust - An Elysian Tail) - What I loved most about Dust is we had a real inversion of values. If it's cliché the vilain to force the hero to fight against his closest friend in order to torture him psychologically, here the opposite happened. The Moonblood Elder made general Gaius fight against the one who was his closest friend. For once I had pity of a vilain when I watched Gaius trying to convince Dust that they were once friends.
Safer-Sephiroth (Final Fantasy 7) - The man used a special attack that destroyed half of the Solar System just to inflict a ridiculous amount of damage. I can't decide if this is sad or funny.
Ultimecia (Final Fantasy 8) - Hard to beat because she was always full of surprises.
Personally, I really enjoy the bosses of Warhammer 40k Space marine, but that might just be the sheer fact that I am an Ultramarine bleeding over.
Mostly, though, I usually don't remember boss battles that much. I usually like the odd encounters that turn into weirdly cool things
For some reason, Icon of Sin from Doom 2 comes to mind. Though I'm not sure that boss battle has really stood the test of time.
Let's see, what else is there...?
There's the champion of the Pokemon League (in any Pokemon game ever)... The rebel flagship in FTL... Doomsday in Sonic 3... Ballos in Cave Story... GlaDOS in Portal...
I'm sure I could think of some others.
The most challenging boss for me was Yiazmat from Final Fantasy XII, it took me eight freaking HOURS, just to kill the final mark, for that little Moogle in dalmasca, was it worth it ? I think it was, the sense of achievement I felt after dealing the final blow was just epic and no boss battle ever since has made me feel the awesome struggle for dominance ever since, not even Dark Souls
Maleficient in Dragonform in Kingdom HeartsThird Fight Riku Kingdom Hearts
But i was really young when I did this battles and didn't use the right equipment. If I 'd try it again I would be probably capable of defeating them with ... less rage.
Zexion in KH2 because of the time limit
Efrey or how this fuckin' thing is called in Final Fantasy X. Hardest Battle in a game I can remember.