Well you could assign them to control groups I suppose. Whenever I build novaliths I always assign each of them a number so it shouldn't be too hard to lump them all together.

That is one thing I really wish we had. A button or little sub-empire tree on the interface that lets us keep track of things like superweapons, scouts and colony ships. Whenever I build those I always end up digging around to find them which is a total pain in the ass.

Simple improvements like a circle that slowly dissapears the longer a planet goes without being scouted, or a symbol akin to the capital planet tiara thing that denotes the presence of superweapons. Clicking on the tab would also select all of them in the gravity well. Perhaps shift click could select all of them in your empire and that would solve your problem.

I agree with Twin Snakes, I generally set my Nova's to auto-fire once my primary enemy is gone.(I play on large, multi-system random maps, so it takes 10-15 minutes for my enemies to notice anyway)

Koda0