Long time lurker, first time poster. I had to jump in on this.
One guy mentioned Goner and I have to second that. Those guys treat you like your standing across the counter. Went to Gonerfest this year and introduced myself to the owners, they went out of their way to make me feel at home. They have a message board to. It's a small community as well as a store/label.
Other good ones
Green Noise
Permanent Records
Certified PR
Trouble In Mind
Not so good
Columbus Discount Records (singles club is a trainwreck, it's a shame, cool records)
Tic Tac Tottally (to be fair he now lets Midhaven do his shipping so it's probably better)
All of those I've ordered from at least twice. I wouldn't really judge on one order unless it was just atrocious, I understand that shit happens.