We added a version of power nullification to our BnV game that was a ton of fun, so I second the whole Rogue-like thread.
Other suggestions...
Add a "sidebar" for powers such as Absorption and Deflection that gives a quick-n-easy system of converting "mundane" damage for use with those powers (i.e. non-powers related damage, such as from a 2d8 gunshot vs. physical absorption, etc). It's can be a fun option for a "grim-n-grittier" game.
Add a guideline for special cases where a superhero's power and a piece of gear are intertwined and not really seperate, such as Captian America's shield, etc, that can be used without too much hand-waving. We used a homespun addition to the way Disadvantages worked that did the job fairly nicely for us, but the system we used by itself could be easily taken advantage of by the cheesier of metagamers.
There were a few other things that escape my mind right now, I'll post up more if you dont mind me going on about 'em.