WoW is a good one. Another reason would be because it made a lot of people far too addicted to it making it severely unhealthy. I feel it's a game that we're better off without.
I think this is the case with Call of Duty and the FPS genre right now, as well as the Fighter genre with Street Fighter (I don't know if that's the best example, though), but to a lesser extent.
FPS and MMOs existed before CoD and WoW. Street Fighter, on the other hand, defined the fighting genre, and made it better and what it is today. Though there are cases were anime 2D fighters are bashed in tournaments, but I think that has more to do with them than Street Fighter, because King of Fighters and Ultimate Marvel vs Capcom 3 are hugely (and rightfully) popular. SFxT is also hated.
Thinking about it, maybe Marvel vs Capcom 3 shouldn't have existed and we should have just gotten Ultimate Marvel vs Capcom 3 in the beginning. :P Much more balanced and better. (Though we could have gotten MvC3's original UI.)
Here's a game that makes me think "wait, why do you exist?" I wouldn't erase it though, since I LOVE it.
On the other hand, this shouldn't have existed.
Before I look like a Sony fanboy (:P), I love Halo, and Halo 3 is one of my favorite games. But this game killed the franchise for me, and to a lot of people.