I've only come across Plan9 in Richmond, Strangeland in Annandale, Smash in DC. Any more I should know about?
Skinnies Records in Norfolk, VA. It's amazing! You do have to dig around for what you want, and the owner is a punk-rocker, and can come off as intimidating, but once he knows you're a real fan of good stuff, he's awesome. They have some amazing old Grateful Dead and Pink FLoyd.
I don't know about any place that sells exclusively records (and I've been looking!!) but I know of some thrift stores that have a collection of records and one antique store in Herndon called Roaches in the Attic that has a decent collection, where I recently bought a Rolling Stones album. But I'd love to find some true record stores!