I'd say "Hijacked by Ganon", which means you spend the entire game knowing who the villain is, have one fight and then they get pushed aside by the final boss/true villain.
Some examples:
Sonic Heroes: Everyone's going after Eggman for different reasons, only to find out that Metal Sonic was the one behind the world domination plan.
Yoshi's Island DS: Kamek is kidnapping babies all over the island. You think he and possibly Baby Bowser are behind this, until it turns out it was present day Bowser.
There's also the misunderstanding cliche. The players and the main character think the villain is once again causing trouble, but it turns out that they weren't really doing anything wrong, or worse, they were the ones keeping the real villains locked up. Most common example would be King Dedede, where he's bathing in the Fountain of Dreams, and Kirby thinks that's the reason why no one is having dreams anymore when in fact, Dedede was keeping Nightmare sealed away. Kind of overlaps with "Nice Job Breaking it, Hero".
Last one I can think of at the moment is when a new villain who has no alligance to the main villain ends up dead, arrested, or for some other reason, gone and never to be heard from again after they've been defeated.