My favorite shop has got to be One Drop Records on Florida Ave. in Washington DC!! They get reggae records straight from Jamaica almost every week, and got some real hard to find shit that you can't really get anywhere else. Another great reggae store in DC is called Action Pack, on a nice weekend when the weather's good they will set up the speakers and play music for the whole neighborhood, you can hear the reggae blasting for blocks!
City Lights, and Arboria Records in State College, PA are two other great music shops. They sell new & used records, tapes and CDs and have a lot of hard-to-find stuff too. I've been going there since I was about 14 years old....