Truly an impossible question... I'm very indecisive hahaha. I also tend to judge how much I like a boss based on how awesome the battle was, so there's that.
Just Listing a few that come to mind, in no particular order.
Brave Fencer Musashi (PS1): Steam Knight, by the gods this boss sealed the deal with me for this game when he crashed through the sealing.
FF 8: X-ATM092, no I didn't google that, to this day I still remember that damned spider's name, oh good times haha.
FF 10: Yunalesca and Jetch, pretty much self explanatory, plot tension, epic music, and epic multi stage fights.
Devil May Cry Franchise: "insert any fight with Vergil/ Nelo Angelo", I'm serious, ANY!
Portal: GlaDOS, because she's a potato.
Dark Souls: Ornstein and Smough, Rekting casuls since 2011 I guess.
Witcher 2: The Kayran, I know this one sounds weak, but for some reason I really liked it. Sile screaming at you from above made everything more tense and epic.
Resident Evil 5: Wesker (Not including Uroboros form), as much as this deviated from the series' roots, there's no denying Wesker was awesome, fighting like a man instead of running away makes the fights 10 times more enjoyable. I really hated how they killed off Wesker with plot induced stupidity, but that's a tale for another time.
Resident Evil 4: Krauser, knife only anyone?
I'm sure I've forgotten a lot, but man you got me swimming in a tub of warm nostalgia now, thanks.