I frequent a number of different thrift and Salvation Army stores and I have yet to find a single Atari game "in the wild."
That being said, I've gone home with loads of NES, Genesis, and Saturn games! ... and I've nabbed a couple of systems as well. The prices are usually rather skewed, but if you find the right employee, you can haggle.
It should be noted that sometimes small items (that people would be inclined to steal) like game carts are kept behind a counter (even if they're only priced at $1.99). At one thrift store I go to, they keep all of their games in a glass case near the costume jewelery. ... they don't even display them so you can read the end labels - they're just all shoved haphazardly into a plastic bin - but you need to nab an employee if you want to rifle through it.