Favorite hero/villain pairing:
I waffle somewhat on hero/villain pairings, because a lot of the ones I like are more hero/frenemy than hero/villain. Harry Dresden/John Marcone from The Dresden Files
, which I love, is a good example. Marcone may not always be a stand-up dude, but the reason people ship the pairing is because he always has Harry's back when Harry needs him, even though they pretend not to like each other (of course, Harry also spends more time describing with vivid 1st person detail what hot stuff Marcone is than any fanfic could; that's part of why people ship it too).
For me, I guess the core of the hero/villain pairing is that Character A could turn good for Character B under the right circumstances, and it gets hard to call them a villain when your little fannish heart is sure they didn't have to be if the hero had played his/her cards right (I'm looking at you, Clark Kent. Remember the early days of Smallville
when everybody was writing the oh-so-sweet futurefics where he and Lex get to be slashy BFFs forever because screw Superman canon? You could have had that, Clark. You could have had that). I like Boyd/Raylan from Justified
a lot too (and the Ava/Boyd/Raylan OT3, of course). Boyd isn't really a villain on the show, but he is pretty unapologetic about his crime lord status. He and Raylan may help each other, but they're always gong to be on opposite sides of the chessboard, and I like it that way, so I guess that's the pairing I'd pick for this one.( The rest of the meme )