All the world loves M&Ms
I found Mutants and Masterminds from Green Ronin to be a pretty thoroughly enjoyable way to handle Supers campaigns in D20 - Marvel, DC, or other. We played a "generic" campaign, and I played a character very much like Iron Man, while my son had literally built up Martian Manhunter. Mechanics worked very well, if maybe just a tad weak on the purchasable equipment side of things. (Super-equipment is dealt with as a point buy power just like "inboard" powers.)