One of my biggest pet peeves is stupidly overpowered villains. I'm thinking Darksied from DC Comics (and his counterpart Thanos from Marvel), the Colossal Titan from AoT, or the Condesce from Homestuck (not counting Lord English from the same comic since he rarely appears). More often than not, they have an absurd array of abilities, are capable of killing major characters en masse, can brainwash characters with absurd ease, or even all three of these at once. When these guys come in, you can guarantee that if the heroes ever defeat them at all, they'll get fucked up by the villain over and over again until the last five minutes of the plot. They're like Mary Sues gone bad.
People who write these types of villains seem to have realized that it's bad to have invincible heroes, but they go overboard in "correcting" the problem by introducing a villain who spends all his screen time shredding the heroes, resulting in an equally unsatisfying battle (since, after all, a guaranteed villain victory is just as predictable as a guaranteed hero victory). They don't necessarily ruin a work completely with their presence, but they're still incredibly irritating to see.