In practically every Story Arc in Bleach, Hollows are involved in some way, shape or form. In the very first one, they're worked in a Monster of the Week format. In the second arc, they appeared as Elite Mooks in flashbacks, and in the very last act, a group of Giant Mooks showed up to transport the Big Bad to their dimension, Hueco Mundo. Following that, we're introduced to Hollow-Shinigami hybrids called Arrancars, who take over the scene as a War Arc erupts between them and the Soul Society. Hell, in the Deicide mini-arc, said Big Bad used the Hogyoku, the same device that created the Arrancars, on himself, but it gradually turned him more Hollow-esque with each transformation. Even in the latest arc, where the antagonists are essentially superhumans, said superhumans only gained their abilities because Hollows attacked their pregnant mothers in the first place.
The Skruggs of Heroman fill this role from the simple fact that they NEVER. EVER. Seem to stay beaten.
The Beastmen are this for the first half of Tengen Toppa Gurren Lagann. After suppressing the humans underground for who knows how long they had it a long time coming too.
Comic Books
Nazis in Hellboy. Of both the Steampunk and magical varieties. While the larger threat is always from Eldritch Abominations, the various Nazi factions have a bizarre habit of being involved with almost every story arc in one way or another, even if the arc had nothing to do with them. One chapter hung a lampshade on it when Roger and Abe find (an utterly inexplicable and with no plausible or possible reason for even being there) a Nazi submarine in the ancient tunnels of a lost civilization beneath the Himalayas. They aren't remotely surprised; the damn Nazis have shown up everywhere else.
The "stupid stupid rat creatures" from Jeff Smith's Bone.
Averted with Marv of Sin City fame who enjoys fighting hitmen. When he goes up against hitmen, he becomes positively giddy since "no matter what you do to them, you don't feel bad."
Film
Indiana Jones makes his thoughts on this trope clear:
Indy: Nazis. I hate these guys.
Literature
In The Hitchhiker's Guide to the Galaxy, Arthur and Ford haven't seen the last of the bloody Vogons after getting thrown out of an airlock by them. Vogons don't like leaving jobs unfinished.
The original orcs of the Lord of the Rings and The Silmarillion are distressingly numerous and fertile, and they will not stop attacking humans, elves, and dwarves even when they aren't enslaved by the current Dark Lord.
The Peacekeepers from Farscape fulfill this rather nicely. They hunt down the main protagonist for two seasons under one crazy commander after another for what amounts to being in the wrong place at the wrong time. And then things get worse.
There's hardly a person in Andromeda who doesn't hate and fear the Magog. Being the followers of the living embodiment of a dead galaxy, those reactions are well earned.
The Romulans were closest to this trope in the series overall; the Borg made relatively few appearances, the Klingons weren't enemies anymore (though individual Klingons often were), the Ferengi were quickly pushed aside, and the Cardassians only showed up towards the end of the series.
Despite the quote at the top from The Simpsons, in the original Star Trek the Klingons made only about three or four appearances in total. In Star Trek: Deep Space Nine there was even an episode where all three of lead Klingon villains from each episode showed up, which demonstrates how rare they were. They are more common in the movies but even then, it was usually rogue elements rather than The Empire itself.
On the other hand, as the show went on every third episode Recycled Script, so while the bad guys in a given story were technically different, they tended to be extremely similar to villains from before and had almost identical schemes; the usual type of advesaries were very common.
Nobody in the Firefly universe much cares for the gorram Reavers. Given their tendency to rape people to death, eat their flesh and sew their skins to their clothing (and not necessarily in that order), this is quite justified.
In the default setting for Dungeons & Dragons, undead are often portrayed as the most hated creature type in the setting, even above fiends. Sometimes, even neutral deities will encourage their followers to wipe out any undead they find. A quote from a cleric states that he fights dragons because he wants to. He fights undead because he has to.
Tolkeen was a peaceful, accepting, integrated kingdom in a mainly magic-based society. The Coalition States went to war with them, forcing them to leap off the Moral Event Horizon in an effort to survive. It ultimately failed. This is not the first time the Coalition has done this. Similarly, Free Quebec was actually a member of the Coalition, but felt they were getting sidelined, and quite possibly lied to, by the Coalition's leaders. All their suspicious were absolutely true, resulting in a costly war between what should have been natural allies. Even for those who think the Coalition might be right, they're hard to love.
At the same time, Chi-Town (founder and seat of power for the Coalition) was pretty tolerant and open until Nostrous Dunscon decided to declare war on them and fling hellish magical High Octane Nightmare Fuel at them. Kinda hard to blame them for thinking magic was evil after that.
In Werewolf The Apocalypse the Garou player characters often have to fight neverending hordes of banes (especially scrags), along with the heaps of fomori and Black Spiral Dancers.
In Exalted, some player character splats can be each others' Usual Adversaries. Notable are the Dragon-Blooded Dynasts and their Wyld Hunt, constantly trying to kill the Solar Exalted and their reincarnations over and over.
Video Games
The Heartless from Kingdom Hearts, which are indirectly responsible for everything that happens in both this game and its sequel.
Speaking of the sequel, Nobodies add their machinations to the mess that the heartless started.
While it can be applied to Beastmen as a whole, it's generally Quadav, Orcs, and Yagudo for Bastok, San d'Oria, and Windurst respectively.
Tsukihime: Vampires. Except Arcueid. Mainly because all the vampires shown except Arc are completely fucking insane and very deadly. Arc, on the other hand, is a cheerful, huggableCloudcuckoolander. Unless you're Ciel or have any connection with her at all.
The Noxians inside League of Legends have a general belief in Chaotic Evil and success by whatever means necessary, causing them to support and aid many clearly bad people to become champions inside the universe, or harm many others which then pisses them off enough to become champions also.
Mass Effect 1 had, in the past, the Rachni and the Krogan threatening the galaxy's extinction for centuries. Now, it's the Geth popping up everywhere, threatening civilization as we know it, though several krogan clans work with them.
In Mass Effect 2, the main enemies are various N.G.O. Superpower mercenary groups, like the Blue Suns. Unlike the Collectors, the true antagonists of the game, the mercs are never really acknowledged to be that big of a threat by anyone, but they're everywhere, and usually stand in the way of whatever Shepard's team wants, especially when it comes to the loyalty missions.
And in Mass Effect 3? Cerberus themselves become this. The Reapers are the Big Bad, and the various forms of husks are their main mooks, but Cerberus just hounds Shepard's team everywhere they go, from Mars to the salarian homeworld, trying to screw up whatever Shepard's team was trying to accomplish..
Cyborgs in The Dishwasher. By the time of the game, about the only people that like them are themselves and the people (trying) to use them. About the only sympathetic cyborg we see is Yuki, the Dishwasher's stepsister. And even then, only for a time.
Touhou has the Fairies. They seem to have no aim in life other than to wear you down before you face the boss of the current stage. They are nowhere near the nastiness of other examples in this page, it's just the thing fairies do. Oh, and don't feel bad about shooting them down, they are effectively immortal.
Just about every canon campaign in Battle for Wesnoth has the player fighting either Orcs or the undead. Even the one in which the protagonist is a necromancer.
The varied and sundry species of Windbag in Bastion, which are all technically different stages in the lifecycle of the same lifeform. They used to live underground and not bother humanity much, but now there's no underground left and they're vaguely aware it's humanity's fault, so they're sort of pissed. Also, humans kind of use Windbag nurseries as power sources, which they're probably not thrilled about either.
In Fallout: New Vegas, the Fiends serve as this to the NCR troops of Camp McCarran and to the Mojave as a whole. The player can accept bounties on their leaders that will end up weakening them and lead to their defeat in the epilogue.
