Most Annoying in-Game Enemy.

[Sir Reginald Bathwater]

Revenants and Chaingunners in Doom 2 - Especially in the Plutonia mod in Final Doom, where they are everywhere, and you have to rote learn a level's enemy pattern. I did manage to beat it on UltraViolence, and somehow seem to have developed a sixth sense for dodging fireballs now.
Minion Factories in non RPG games, where there is no reward for killing the minions.
Boss fights which start with a scripted conversation - I cannot count how many time i have been behind an evil wizard with my knife raised, when he suddenly goes on a rant about how evil he is, THEN i lose my stealth-kill opportunity, and get served with a glass of ownage.
Magic-resistant enemies, especially those whose resistance is 'natural' and cannot be reduced.
Shooter stacks which block your exits in HOMM.
Ghosts in HOMM, or other undead which convert your soldiers into more of them - Especially when you have peasants in your army.
Generic rats/goblins/spiders/bats which waste your spells/mana/ammo.
AI-enemies who can see through bushes, or other non-solid obstacles.
Pyros/Demomen/Heavies who spend the ENTIRE round being an engineer's ***** and killing spies who enter the base.
Finally, players who (on either team) set up on the final objective from the start of the game.

 

[The Shade]

Either the Flood guys that shoot spikes at you in H3, Giant Radscorpions (or Albino RadScorpions, now), or Super-Mutant Overlords when you're level 30. Those bastards will massacre your sidekick and never FREAKIN' DIE! (Unless you have a Fatman. Which I do.)

 

[Mr. Fister]

The Red Arremer Ace from Super Ghouls 'n Ghosts is one of the worst enemies I've ever fought in gaming. He's the personification of why that game is hard for all the wrong reasons. He has a totally unpredictable pattern, swooping down and firing projectiles at random. He's also a master at dodging your attacks at the last second when he's not already out of your weapon's limited reach. The worst part about him is he's usually close to the checkpoint when you fight him, which means if he kills you (and he probably will), you have to go all the way back to the beginning/last checkpoint just to see if you're lucky enough to beat him this time.

 

[0thello]

I managed to get my hands on ICO yesterday (real cheap and in mint condition) and the shadow monsters have got to be the most annoying enemy I've fought in a long time.

 

[Mr. Fahrenheit]

Birds. Any bird...any bird at all! It's unavoidable. If a bird is an enemy in a videogame, it will be obnoxious...

Malboros in almost every single appearance they've had (Except maybe XII. They weren't that bad in XII).

Also, those big jumping robots that can take off half of your health in the first Mega Man.

 

[Srkkl]

Those annoying ass bosses that you know your gonna beat but it takes three hours to kill him. The frustratingly easy boss.

 

[AceDiamond]

Deathclaws. wtf were they before the fallout? Demons?

Exactly.Same with "Giant" Radscorpions. They're already giant!
Also, what explains the fire ants?

Deathclaws = Experimental creations. They weren't mutations.

Fire ants = Regular giant ants. There's a quest that explains their origins. The quest is called 'Those!', and you can start it outside the Super Duper Mart near Megaton.

After I posted, I felt like playing FO3. Then I finished that quest, but still, how did they end up breathing fire? The scientist's explanation makes sense at first, but after some thought......

You have to remember that the Fallout Universe runs on SCIENCE! not Science.

Also, while it's true they are genetically engineered, the Deathclaws were originally Jackson's Chamelons before being given some form of DNA cocktail.

 

[letsnoobtehpwns]

Flood in all the Halo games.

 

[Anarchemitis]

i cant hit a headcrab worth s***

Fast Headcrabs are moreso.

 

[konkwastaken]

last mission of armored core for answer, you gotta take on 5 NEXTS on your own, when i was still noobish at it i could barely kill one or two before dying.

Laser blades and Assault Armor, that's what I used...so cheap.

I used assault armor and kojima weapons, pretty cheap too

 

[kaljtgg]

Does Navi count?

 

[Juan Regular]

Those godforsaken ghosts in Silent Hill 4.
There's nothing worse than enemies that can't be killed.

 

[Thyunda]

Deathclaws. wtf were they before the fallout? Demons?

Exactly.Same with "Giant" Radscorpions. They're already giant!
Also, what explains the fire ants?

Deathclaws = Experimental creations. They weren't mutations.

Fire ants = Regular giant ants. There's a quest that explains their origins. The quest is called 'Those!', and you can start it outside the Super Duper Mart near Megaton.

After I posted, I felt like playing FO3. Then I finished that quest, but still, how did they end up breathing fire? The scientist's explanation makes sense at first, but after some thought......

The game is about a guy who lived in a hole in the ground to avoid the nuclear apocalypse, and you think fire-breathing ants are far-fetched?

 

[CheeseSandwichCake]

Either the Flood guys that shoot spikes at you in H3, Giant Radscorpions (or Albino RadScorpions, now), or Super-Mutant Overlords when you're level 30. Those bastards will massacre your sidekick and never FREAKIN' DIE! (Unless you have a Fatman. Which I do.)

They don't massacre your sidekick if he's Fawkes.

Oh right, cheapest in-game enemy? The only thing coming to mind right now is the Krogoth but there's probably something more BS lurking in my memory. I hated the missions in the campaign as ARM where the enemy just threw the things at you, since they had like 100k HP and you don't have a similar unit to counter it with.

 

[Halfbreed13]

Does Navi count?

HEY! LISTEN!

 

[GuerrillaClock]

I think the Flood Stalkers from Halo 3 pissed me off the most. Especially on Cortana, where they climb up onto the ceiling and shoot at you.

Have to agree there, especially since they never seem to stop to reload.

 

[Woodster 117]

Quick Time Events.

And if those arent allowed i would have to say the Jackal Snipers with Beam Rifles.On Legendary difficulty.

Damn they were annoying.

 

[Internet Kraken]

I seriously hate Gyrados in Pokemon right now.

It's intimidate ability cuts your attack in half. You do little damage to it's already high HP. Combine that with all the ridiculous moves it can know, like hydro pump and ice fang, and it becomes even harder to kill. Also, it seems like every single water type trainer has one of them.

They annoy me more than any other Pokemon in the game, and they don't even inflict bullshit status conditions.

 

[SovietSecrets]

The dogs from Call of Duty 4 on veteran. Hit that button too early or too late, especially on the flashback level in Chernobyl, anger rises quickly.

 

[AkJay]

Any enemy wearing that unstoppable, bullshit armour on everything but that one spot on their back. WTF is up with that?

Like those ice dinosaurs from Metroid Prime? yea, they pissed me off.