Anyway, with that out of the way, on to the idea seeds:
1) Villains Win! It's just not a comic book thread without somebody suggesting this. You know how it goes. The sexy heroine goes to foil a bank robbery/gold heist/whatever only to be beaten/hypnotized into submission and abused every-which-way. I'm willing to play this straight, or subvert the hell out of it if you want: I don't really do subs, but maybe the villain's control isn't as absolute as he thought, and the scene ends with the villain getting pummeled to within an inch of his life. Or maybe the heroine is so broken that the next step is an evil costume change (mmm, leather).
2) It Came From Planet X! It's also not a comic book thread without a monster of some kind. A tentacle beast? A reptiloid? A talking monkey? Giant ooze? Whatever it is and wherever it came from, it's drawn to spandex-clad women like...well, like a talking monkey to a Superman cover.
3) Necessary Evil Aliens successfully lured all of Earth's superheroes to one place, and killed 98% of them. This puts the world's supervillains in the awkward position of having to fight off the alien occupiers. Because you can't very well rule the world if some Grey has taken over, now can you? The RPG I stole this idea from was set in I Can't Believe It's Not Marvel, but I'm willing to do it in 'actual' Marvel or DC if desired. This would probably be a non-D/S scene, with characters forced to work together for the greater (blegh, I almost can't say it!) good. And maybe finding out that they like it.
4) Hoist By Her Own Petard Sort of a subset of the first idea. A gadget-using heroine finds that somebody's stolen some/all of her widgets and is fully prepared to use them on her. The most obvious example I can think of is Wonder Woman getting tied up with her own lasso, but I'm sure there are other ways this could be done. Also works for an animal sidekick gone wrong.
5) Power Overload Something happens to make a heroine/villain with the right powers go berserk. By 'right' I mean something that would lead to interesting results; somebody with plant powers is constantly accosted by vines, somebody with emotional or mental powers is constantly dodging people who desire her above all else, things like that. Who did this to her, and can she stop it before she succumbs?