You're not the only one who'd love to play or run a Mutants & Masterminds game. I've had a bunch of ideas for running a game, myself, but doubt I'd ever get the chance. Anyway, here're the ideas I've had.
1) Super-Heroes/GURPS IST - I actually don't like the GURPS IST world. It annoys me to hell. But then I looked at rec.games.frp.gurps and I saw a poster there by the name of Joseph Justice and the things he'd done with his campaign, and I was suddenly inspired to take the GURPS IST world and, using the base setting, add things on to it to make it into a world that I could like. Think of it like this: Part of the challenge was creating a world which I could enjoy while using the foundation of the IST world (Of course, that may not be for everyone, but I like that sort of thing. I purposefully sabotage myself for the first couple of minutes when playing Tetris, for instance, just to see if I can get out of the mess I made). I came up with some pretty good ideas, in the end, and liked how the IST world would have looked like had I been able to run it.
2) Super-Heroes/Homebrew - Also came up with ideas for my own world. I've got something in the area of 30-40 super characters of various types made up to one degree or the other for the purpose of using them in a homebrew world.
3) Super-Heroes/DC Universe - I also considered a campaign set in the DC Universe. The plus side to this is I could order the DC HeroClix figures, rebase them, and then all I'd have to do is write up the stats for them in M&M terms. I like the DCU, so it seemed like an appealing thought to me.
4) Sci-Fi/Fantasy World - Ever watch He-Man and the Masters of the Universe? I had an idea for a fantasy world with orcs, vampires, dragons, and magic, but which also had elements of higher technology.
5) Transformers - My own version of the Transformers universe. Every player plays an Autobot, and they fight against the Decepticons as well as other enemies.
Just some ideas I had.