East Village Books is one of my favorite used bookstores, and even if I'm not in the market for a new read I usually find something worth buying. I love the "bargain" shelves because the books - usually $2-$4 - are actually good ones!
The CDs and movies are sometimes overpriced.
They have a hearty selection of underground and anarchist publications that you definitely won't find at Barnes and Noble.
Prices are fair, and stop in to see the copy of "The Man in White" by Johnny Cash in the case behind the counter.