I've only bought a couple items on MusicStack, but the experiences have been extremely positive. Unlike some other sites, MusicStack requires a minimum number of items in a seller's store (500 items, I think), so your selection there is generally from professional dealers rather than clueless people clearing out grandpa's attic.
There's also GEMM.com. You'll find a lot of the same MusicStack sellers on GEMM, but you'll also find people like ... well, me.
SFH Records - prog, fusion, folk & more: http://sfhrecords.gemm.com/