The only Atari games I've come across at a thrift store or yard sale were 5 5200 carts. They were all commons and pretty bad games at that, but I bought them anyways. I don't even have a 5200 (I have a 7800, woot!), but I was so surprised to see Atari carts that I snapped them up. Other than Atari, I come across NES, Genesis, and Master System carts once in a blue moon at my local DAV thrift store, and once at a yard sale I found a Sega Game Gear (it was too expensive though). If you have a Play N' Trade, they sell Atari carts relatively cheap. I got a near mint "One-On-One Basketball" 7800 cartridge for $0.25
I live in VA, by the way, and it does seem as though the Atari craze of the 70's/80's just passed right over my whole area...