Good villains

So I was watching something comic related at some point recently, I can't remember what it was though, may have been The Super Hero Squad Show, maybe Young Justice or another of the Cartoon Network shows, and was wondering what villain the characters were talking about. They were talking about how even the the villain[s] was doing bad things, that maybe he thought he was good, while the hero was actually the bad guy

Its hard to say for this specific episode since we dont know wich one, but it sounds like a speech that can be made for a big portion of all villains.

I have decided that it was Ben 10 [I don't know which incarnation though] where all the villains team up in an effort to try and stop Ben, at least I think it was Ben 10.. .. Wait. No. What was I thinking.. Now I am pretty sure it was Doctor Who and the episode was probably The Pandorica Opens. I'm not 100% sure of this but close to it