If your talking about overall species I would have to say Cazadors, But if you were talking specific person id say I hated Colonel Autumn the most from Fallout 3, really grinded my gears. And if you mean faction I would have to say Caesars Legion just based off of their brutality and the way they conduct themselves.

Cazadores for New Vegas, and Feral Ghoul Reavers for FO3. I do have bad memories of Reavers back in Point Lookout, and Cazadores are well...Cazadores ._.

Most hated enemy in New Vegas is definitely those Ghost Trappers in Dead Money because they are such bullet sponges and hop around like Bunnies on Crack.
In Fallout 3, most hated would have to be the Feral Dogs that seemed to appear everywhere.

I hate Cazadores the most because they're annoying little buggers. Caesars Legion grinds my gears because of their actions.

I have to agree the Cazadores, and in the lonesome Road those damn tunnelers....

The first place goes to the cazadores, without doubt, the nasty buggers take a lot of HP out of you and also poison, and second place are centaurs and lakelurks, oh those UGLY fuck*rs scare the sh** out of you when they come out of nowhere at night.

That must be the centaurs,they are not hard to kill but the thing is freaky

cazadores, especially when there is one cazadore there is bound to be more of its friends laying in wait.

I hate the lakelurk because their sonic attack damages considerably our stuff and for low level, it removes half of health.

I'd say centaurs are my most hated enemies not because they're difficult to fight but their original design is pure nightmare fuel. No matter the game whenever I see them I get away as fast as possible.

Cazadors by far especaily when i don't have any antivenom.

The kids you accidentally shot and you can't fast travel or sleep or wait.

Fallout 3 would be the Overlords, I. HATE. THEM.
They are just a bunch of bullet-pin-cushions and always have some heavy weaponry to annoy me with. They are even worse in TTW, where they carry Light Machine Guns.

In Fallout NV including the DLC's, I would say that the tunnelers in lonesome road and the ghosts in sierra madre are my most hated enemies.

Vanilla wise, in New Vegas, I'd have to say it's the Deathclaws. Those suckers are bullet sponges, fast runners, and odds are, they'll see you long before you see them, which usually ends up with you getting hit in the back and killed before you can turn around. DLC wise, it's definitely the Robo-Scorpions. Goofy, I know, but those things are tough little beasts. They're numerous, have pretty high DT, and have those laser tails. Not to mention the first time you kill one, you're likely to run forward, only to get hit by its self destruct mechanism.

In Fallout 3, it's definitely got to be the Super Mutants. They're numerous, and odds are you'll encounter them at a really early level where you're underequipped and poorly armed. I recall being a level four and running into them. All I had on me was an assault rifle with a few rounds for it that I got out of the Super-Duper Mart after a relatively heated battle with the raiders within. I don't know how, but I managed to bring the two down and I had about six health points left by the end of it. But I was a minigun and a hunting rifle richer from the experience, not to mention the experience points themselves.

Deathclaws and Cazadores by far. You simply just cant hit them outside VATS.

Hands down are the cazador's. For w/e reason they creep me out and are the worst enemy for me. Deathclaws i think are cool and I can handle, but the cazadors are crazy strong and fast, capable of flight. The ultimate freak of nature! lol

I honestly hate Geckos so much. They run weird, and just annoy the crap outta me! I mean they are a easy low level enemy, but they just pester me like CRAZY!

Cazadors in New Vegas, Radscorpions, especially them Albino ones in Fallout 3 and Floaters in Fallout 2

bloat flies, they're just an annoyance to me. Sure they're fun to blow up but is it really worth hearing bzzt bzzt every time you're walking around.