That One Boss

Flowey.
God I hate Flowey.

Nah said:

Any boss that has other enemies around to help it (hello Capra Demon in Dark Souls and Gargoyle in Xenosaga 1, you can fuck off). Fight is usually bullshit when the little helpers are around, but once they're dead the boss is usually not terribly threatening.

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If you want bullshit, watch this analysis of Four Kings: https://www.youtube.com/watch?v=F2MSaKOIvXQ&t=46m20s

Silent Hill 2; haven't actually seen any of the bosses, but 'dread' going anywhere near them.
Ghetsis in the first Black and White games I thought was pretty hard. I've played through that game several times with numerous different teams and never been able to get past him the first time.

The 7th boss of Furi, The Burst, the sniper boss. I'm sure everyone who played through Furi already knows this though, since it is considered the hardest boss in the game (okay the last one is harder, but it is the final boss of the game). Her sniper shots are 1 hit kills and she gives you only 5 seconds to find cover. Bosses in Furi are separated into phases, and while her first 5 phases aren't too bad, her last phase is ridiculously hard.

https://www.youtube.com/watch?v=3ulxY-CRH0k

Basically you have to dodge bullet hell while hiding from her sniper shots. And losing a life in any part of this phase (even after the worst is over) will make you do it all over again. Makes it all the more satisfying to finally beat though.

Shame the 2 bosses after her are pushovers.

Could never get around to beating the Demi-fiend in Digital Devil Saga. I mean, right off the bat, if you have any skills that nullify any of his attacks, he uses Gaea's Rage instantly and KO's your party, lol. I tried about 15 times and couldn't come close. Not to mention he has has two demons present annoying you with various death/status spells. One screw up and it's game over. :(

Deus Ex Human Revolution is one of my favorite games of all time... But I hate Yelena Fedorova.

Seriously her fight is probably my least favorite part of the game. The bosses in general are really... not good, tbh, but her fight is probably the worse in the game.

Touhou Puppet Dance Performance. Base Game. Remilia.

she caps out at 40 when the boss immediately before her caps around 30, and has a pretty tough team even disregarding the level spike

also demyx, of kh2 infamy

or saturos, in golden sun 1

or that one trainer on route 103 in world link that has what basically amounts to mew i say that as if i'm ever gonna play vanilla wl again

really, i could do this all day_{^{barkeep get me a glass of brain bleach please}}