Lets see...
Those giant legs in Dark Souls that chase you over lava(I can rant about this all day)
Those dragons in the Valley of Drakes in Dark Souls that shoot lightning at you
Those fucking ninjas that chase you in Mirrors Edge
Any minibosses on Bayonetta on the hardest difficulty, especially those two fuckers with the claws that love to gangbang you while zapping you & lighting you on fire.
Gekkos in MGS4 before I got my railgun.
Skeletons from Dark souls without a divine weapon.
Little adolescent fucktards with goddamn mics that love to keep it at max volume & yell, laugh, & SING over the shit while the game is in session, effectively making it so I cant mute them until a window presents itself. Also, that complain & bitch alot when you beat them/dont let them piggy back off of you. Fucking kids.
& Most of all, those goddamn bees from Star Ocean. They've bled over into WKC2 as well as vesids but in ANY Star Ocean that they appear in those bees will ruin the Hell out of your day.
The shillings that fire giant blue beams in Gundam Extreme VS. Barely any damage, but stuns on hit, averaging 6 seconds to get hit, get downed, recover, and be able to mov again. That and having a dozen of them on your ass at once while trying to take down the DX Gundam. FFFFFFUUUUUUU-
If you played FF13, you encounter a Electric Turtle enemy of a sort, where you have to fucking stagger just to flip that bitch over and beat it to death.
Enemy recovers from Stagger quite quick and the damage it does is high
At least they were manageable in the first game, in Bioshock 2 they're FAR worse (in that they are stronger, much more resilient and usually attack with other Splicers).
Those parasites that pop out of Ganado's heads on Resident Evil 4
Floows from Super Smash Bros Brawl's Subspace Emissary
Gill and Seth from the Street Fighter series
does human players count as an annoying enemy? if so then I say those human players in multiplayer who abuse glitches like tehran high way in battlefield 3, using teh overpass to make hell on the other team.
AI trolls. Not much more irritating than a program torturing you then giving you the slightest glimmer of hope only to rip it away at the very last second in the most infuriating way.
Btw my experience was recent, & the culprit were the coms on MvC. Shit made me never want to play again.