Graham Hick wrote:In Your Ear
Twisted Village
Mars Records
Newbury Comics
Planet Records
Mystery Train
Nuggets
But I haven't lived there in a long time so some of these might suck now or no longer be there.
In Your Ear is still around but moved over to near Harvard Square. Jeff Connolly from the Lyres used to work there...still probably does. He's usually pretty amusing.
Nuggets is still in Kenmore Square and is still great.
Newbury Comics is good (Newbury Street, Downtown, Harvard Square). They are mostly carrying CDs these days.
In Your Ear and Nuggets are the best bet for vinyl. Mystry Train used to be great but I think they only operate up in Gloucester now. The other shops may still be around but I haven't heard of them.