Topic: Most annoying enemies per series

You couldn't be more right.

EPIC WIN

like-likes zelda series

Mario - Hammer Bros., Boomerang Bros., Bros. in general (except the Mario Bros.), Lakitu
Zelda - Wallmasters, Floormasters, masters in general, Redeads
Kirby - Gordo
Castlevania - Medusa Heads
Duck Hunt - The dog
Metroid - Metroids
3D Sonic games - Bad camera

EPIC WIN x2

Pokemon - Zubat
'nuff said.

WIN

WIN

This.

Final Fantasy: Tonberry's....always grudging on your characters....
Mario: Hammer Bros are ALWAYS annoying...
Super Metroid: The Gold Space Pirates....my god I had to look up their weakness to kill them!
Sonic: Those GUN robots....especially in 06....

Off the top of my head it would be lakitu. He's ALWAYS being a pain no matter what he's doing.

Platformers: Stalking me relentlessly throwing crap on my head.

Mario Kart: Floating right in the middle of the screen making an obnoxious sound and holding a sign when I'm trying to do something "YES I KNOW I'M GOING THE WRONG WAY"

Mario 64: Doing an all around crappy job as a cameraman.

He's just a perpetual thorn in my side.

(Most RPGs) - Mimics
Castlevania - Mudusa Heads and Hunchbacks
Half-Life - Headhumpers

Sonic series: Slicers, Shellcrackers (Sonic 2), Artificial Chaos (Adventure 2, Shadow), Giant Helmet Hammer Robots (Heroes)
Castlevania: Hunchbacks
Street Fighter: EVERYONE!

Any Badnik with spikes. >:[

For me, some of the more annoying enemies I had to face in games were:

From the Mario series:

Phantos. God I hated those things and how they chased Mario whenever he picked up a key. Oh well, at least a star could kill them.

Fishin' Boo. He wasn't a common enemy, but damn that thing was annoying in Choco Ghost House in Super Mario World. And he's even worse when ROM hackers use him.

Meteor Storms/Volcanic Eruptions. You know, like in this level of New Super Mario Bros Wii:

Those things are infuriating. Especially in that New Super Mario Bros DS level where you had to be Mini Mario. Or in Mario Kart's Lakeside Park and Grumble Volcano.

From the Zelda series:

Bubbles. Don't you love not being able to use your sword? Or how some in the original could stop you using it permanently til you hit another one?

Wizrobes. They're annoying in any game, but I hated them most in The Minish Cap where they could set Link on fire and send him running around uncontrollably. Or freeze him in a block of ice. And you had to deal with two or three at once...

From the Wario series:

Those bombs from Wario Land 1 that latched onto your head. Argh... talk about the most annoying kind of suicide attack!

Probably the ghost boss too, it could stun you in mid air, leaving you defenceless from enemy attacks.

From fan made games and hacks

Elite Koopas/Paratroopas. Most annoying things ever, in that they had Chargin' Chuck style health but special attacks to boot. Like throwing their shell at you, turning into a disco shell instantly on sight or charging at great speed. See here:

This gimmick. Go left, you die instantly. Spin jump, you die instantly. Enjoy the ice physics!

And in any game, homing projectiles. Especially in large numbers.

Kid Icarus: Ornes, Mimicuties (due to dodge mechanics)
No More Heroes: Gun Enemies

Mario - Lakitu
Zelda - Like Like (especially in OoT and MM where they pop out of nowhere. >_>)
Monster Hunter Tri - Rhenos (however you spell its full name, lol)

Lakitus in level 2-5 of Yoshi's Island prevented me from getting 100% in that level for 7 years. I hate them and I want to destroy every last one of them. But then you get hurt 60% of the time when you try and kill them, and they taunt you from their stupid smiling clouds...

Ice Keese.

Paper Mario, the Dizzy Koopa (?)

The enemy can put your character into a cycle of endless incapacity, the effect is like being skipped in UNO constantly. It's not hard to see how this is problematic, especially when the issue is compounded (in the N64 version) by partners who can't use items to heal off the damage.