I'm happy to say that a friend of mine just told me about a huge cache of NES and Genesis games in the box that a local game store had. I got Ultima: Exodus and Shadowgate complete in box with instruction manuals and dust sleeves and all that on the cheap, and I also got Contra: Hard Corps and Gaiares for Genesis in box (Gaiares with instruction manual) for fifteen bucks each. I was quite happy, since I've been watching both of these on Ebay and they regularly go for 30-40 bucks loose.
I was quite stoked, I don't remember the last time I saw an NES game complete in box, much less in a store at a cheap price, and much less a whole shelf full.