HL2 is one of the more recent examples of "let's put in alot of enemies that aren't hard but more extremely annoying", as mentioned already:
-Fast zombies = pain in the ass, pretty lame design imo as well. Zombies should always be slow, personal preference. Not to mention the pesky fast headcrabs that strafe your shotgun every time you kill the zombie.
-Poison zombies = how many grenades can a guy take? Slow headcrabs that fall off constantly? Where is my fire weapon valve?
-Manhacks = again not hard to beat, just annoying as hell. Thankgod for the gravitygunslam.
HL1
-Houndeyes = extremely cute when you meet one, but if you run into a pack the sound alone makes you want to kill yourself. Shotgun advised.
-Baby headcrabs = pesky white buggers, they come from a large testikellike sack from mama headcrab and are hard to kill cause they're so fast.
Hl1:OF
-The one eyed enemies with the electrobeegun. They would always hit you 100% because of the incredibly accurate gun, making them a primary target if you ever saw one. Killed me a few times as well when on low health and in bad save spot.
Diablo2
-The creeps/minibosses that shoot lightning from their bodies when you hit them. Especially annoying on hell level where you find a miniboss with this around every corner. One little ball actually contains about 5,6 balls damagewise at least and it hurts like hell. Not to mention if the minions around them just happen to be resistant to your favourite spell.
-The little ratguys that have insane running speed and hit you 10 times asap usually with stun as well when they are near. Little bastards actually killed me a few times ( playing as a caster )
WIIIFrozen Throne
-Blademaster, seriously everybody always picks the fricking imba blademaster. The same applies for ( otherwise fun ) custom maps. The son of a ***** just keeps running away with windwalk every time you manage to actually hit the actual blademaster to low health, with insane fighting speed @ custom maps this makes him extremely annoying to play against.
-Demonmaster, the elf one. Not sure if the name's correct, but you know the one with the manaburn and high rate of attack. Same as blademaster, if unchanged in custom imba as hell.
C&C
-How many hits can a damn gdi mammoth tank take!!!!
C&C tiberian sun
-The hedgehog creeps that spit balls ( or something ) at you, doing insane damage to infantry and light/medium vehicles. What the hell?
-Floaters, not that hard damagewise but just annoying with the constant buzzing sound.
-Visceroid, impossible to kill whilst in a tiberian field and it does insane amounts of damage to anything light to medium armorwise. Especially annoying when one refuses to exit said tiberian field and continues to harass your harvester for ages.
edit: forgot some
FarCry
-The monkeys, just annoying. Not to mention the idiotic "let's throw you out of a chopper with 6 bullets in the middle of monkeyland" section levelwise.
Mortyr
-the mech things in the future section
Dead rising
-Just about any zombie at night is extremely hard to kill imo. B
-Carlito, most hated person here I think. No man can fire a damn 50cal sniperrifle whilst standing!!!!
Kameo
-The guys that hide beneath koopalike shells.