o-- Emerald WEAPON - FFVII - One of my first super bosses.
o-- Ruby WEAPON - FFVII - One of my first super bosses.
o-- Hell Wyrm - FFXII - BIG! One of the biggest bosses I've ever faced. I listed him instead of Yizzy because I haven't beaten Yiz yet, and I want to wait until I do before I list him. Who knows what memories I'll have after beating this baddie.
o-- Xigbar - Kingdom Hearts II - Mainly because of his cool Californian accent.
o-- Sephiroth (last form) - FFVII - I expected it to be harder... (SPOILERS about the battle)
lol at one-hit kill. Lame! Where is that epic battle going one vs one?
Typically, most of the memorable boss battles are from Square-Enix games (specifically SquareSoft before Enix came along). Star Ocean and and any other game never really provided me with any memorable battles.
Ganondorf and Ganon from Ocarina of Time I simply will never forget, it's such an awesome battle even though it's sort of easy.
At the end of Starfox 64 when you fight the Starwolf team and Andross I don't think that I'll ever forget that either I've done that battle at least 50 times, most of those times are from way back in the day when I was really into that game, it's still fun now but I don't play it very much.
Resident Evil 3 - Nemesis Fucking insane and extremely tough, there's not one fight that's easy and not one that's fair. He's faster than you, powerful enough to kill you in two hits, and he can clobber you from far and short distances. The fight in the clock tower yard is ridiculous since you can't tell your health.
Devil May Cry - Mundus Epic. Just flat out fucking epic. I won't even talk about it for sake that some people haven't experienced it.