Is the Doctor Who example a zigzag? First Blon tries to invoke the trope, then the doctor subverts it by lampshading what she is doing, then Blon claims that his lampshade proves that he is no better since he knows the trope all too well not to do it himself, then she attempts to re-invoke it as the dog.

Should this trope be divided into sub-pages?

Pain in Naruto has a literal pet the dog past?

Concerning this example that was deleted:

• Assassins Creed: Brotherhood has a touching moment where Ezio, who is a bit of a jerk even to his friends and allies, finds a young boy who is crying. He sits down next to him and asks him what's wrong, and speaks to him in such a kind hearted and uplifting way that it has to qualify for a Pet the Dog moment.

The trope does not deal specifically with villains. It deals with people who mistreat other people a lot, including Jerkasses.

This trope is relevant to heroes in the same way Kick The Dog can be.

I cut a lot of the Indiana Jones examples because Indy is basically good. There are some gray elements to his character, but he's basically a Knight In Sour Armor. A such, I don't think he really fits this trope.