Nanotech is fun... and a bit scary. It's certainly worth exploring in regard to your Mutants & Masterminds characters either as a way for them to gain powers or as the way in which their powers operate.
It's all about manipulation at a molecular level. Aspects that have clear applications include monofilament and smart materials capable of adapting to their surroundings - perhaps you do not wish to waste time finding a telephone box (if you can, these days) when it is time to spring into action, so you could use smart material that can transform from a business suit to your superhero costume at time of need!
If you want to make stuff using nanotechnology, this probably falls under Inventing, especially if it is not a prevalent and common technology in your campaign world.
There's a whole bunch of ideas here, things that inventive characters can tinker with and any character could use if he could but find someone to make it for him. A particularly helpful application is nanobot 'surgeons' that float around in your bloodstream and repair any injury. If you want to weaponise Nanotech, go for monofilament swords or whips, or concoct an exotic nano-toxin.
The possibilities are endless...