Lot of good advice so far. I agree with Heap in general about making sure that everyone in the group is on the same page in terms of how powerful things should be. It's fair to say "Any power not max'd out, rankswise, is useless," and it's fair to say, "Only max out a power if your character concept makes it not merely possible but necessary." Both are legitimate builds, but if you have players in the same game trying both of 'em, you'll end up with an unfortunate power disparity.
General stuff I've house-ruled:
Invisibility: Right now, it's too easy to get too powerful with just one rank. I rule that an invisible person standing in the open can only be noticed with a Spot check with a DC of 10+ranks – and that, per D&D invisibility, just gets the "Generally around here" vibe, and you need to get 30+ranks in order to pinpoint their location. (That's for moving but not hugely active. For someone kicking up dirt or otherwise making a lot of ruckus, I assign bonuses to the Spot checks, just like the D&D rules for invisibility…)
Skills: I go with 2:1, but from what I've seen, this is a situation that is less likely to be solved by ratios than it is to be solved by a GM forcing skills to be important. That said, I also tend to substitute the skills from d20 Modern, which I like more than the basic M&M skills (although I love Taunt).
The rule about knockback is a beautiful and glorious thing – the one where if you get stunned, you're knocked back a long ways. I would always use this house rule, just to avoid combats where guys stand toe to toe and do massive damage without ever moving. In the same vein, I tried to get rid of the combat mat and allow for more descriptive combats – so that if somebody got hit but made their damage save, I could say that the bad guy grabbed them by the face and slammed them a foot deep into the ground, but then they kicked the bad guy back and clawed their way back to their feet by the time their turn arrived… no real difference, but it sounds more superheroic.
Absorption: It's a bit more expensive than I think it needs to be. Definitely worth looking at in your campaign, but buildwise, Absorption is Protection with the "Only against Energy or only against Physical" flaw, with an Extra of (for example) Boost with the "Only after I get whalloped" flaw. That combination seems more like a 2-point power than a 3-point power.
Incorporeality: Definitely look up the new errata'd version, which is less abusive. But also make sure that a PC who takes Incorporeality understands that, as GM, you are going to have to have that thing they're vulnerable to show up on a quasiregular basis, because otherwise, they're never in any danger.
And as a GM, don't be afraid to go crazy with Extra Effort – and encourage players to do so. I had one player who was ticked off about being stuck in a hallway with bad guys between her and the exit, and she was sure she was screwed until I politely suggested that she use Extra Effort to gain Incorporeality off of her Super-Speed and then describe it as just moving so fast that none of them could stop her as she ran by. When the heroes ran up against incorporeal monsters that were only vulnerable to silver, they used Extra Effort to miraculously notice that some of the statues in the park they were fighting had real silver weapons in their hands, so the heroes yanked 'em free and went to town. It is exactly what your GM-mind would scream "Abuse!" at in a D&D or d20 Modern game, but it's just good play here.