If they're used in one of the video games, there should be minifigures, plain and simple! Supergirl, Batgirl, Nightwing, the Hawks, Brainiac, Clayface, and even Killer Moth are probably near the top of my list for DC.
For Marvel, I think they've done alright with the movie characters thanks to Avengers, but I wish Lego had gotten the Marvel license sooner so they could've capitalized on the Avengers: Earth's Mightiest Heroes cartoon. Ultimate Spider-Man is giving them a nice group of characters to pick from (who'd have thought we'd ever see Iron Fist or Nova before the rest of the X-Men besides Wolverine?), but Avengers: EMH had such a deep roster of characters between the changing Avengers line-up, guest stars, and villains... the possibilities would be endless.
But right now I'm hoping they keep the license throughout the next slate of Marvel movies, because if we get Guardians of the Galaxy sets, that has to mean a Rocket Raccoon minifigure!