One thing that I can suggest for M&M games is that you consider alternate settings. Instead of the basic modern superhero Superman type story, try differing the time period, the acceptance of heros, the nature of superpowers or any other variable youe can think of. Some great comics to look at for different play styles:
Basic Modern:
Stormwatch (the later issues are better)
Changing the world:
The Authority (early issues of the first series)
Non powered cops vs. powered criminals:
Powers
Victorian Era (My Campaign):
League of Extraordinary Gentelmen (the comic, not the movie. Comic is much better)
Coming of Age story:
Ultimate Spiderman
Bigger then end of the world threat:
World War III/Maggedon Story line from JLA (around issues 40 or so)
Vigilante, Cold War, Nature of Heros, Mystery, Faded Glory, and ANY other setting:
Watchmen (this is a MUST read for any superhero campaign. BEST COMIC EVER. Beware: may not be apropriate for younger audiences. If it was a movie it would be PG-13 or R)
Thats what I can think of off the top of my head. Reading any of these should give you some great ideas on how to twist the superhero concept to make your campaign unique.