If the Genesis scene is heating up, I'm not seeing it in my area. Boxed titles are as cheap, if not cheaper then loose NES titles. I'm glad I got a lot of stuff I want for this system out of the way already.
SNES is definately hot. Weather I visit an overpriced store or a store that generally has good deals, the SNES games always command the highest price out of all the cart based systems (with a few N64 exceptions). Even at the flea market I visit, most vendors are asking for a $5 minimum on loose SNES games...
DC is definately hot too. Ever since I started collecting for it 1 & 1/2 years ago, it's been hard to find good & complete uncommon titles, especially the 4 shmups and the dozen or so 2D fighters. I agree that this will be a tough system to collect for in the future, especially if it continues to gain a cult popularity.