I've bought copies of their books at indie bookstores. I don't know that you're going to find a lot of books from small/independent presses at the bigger stores (whatever ones might be left in your area). Distribution will always be a problem there. That being said, the Permanent Press has an excellent reputation for publishing good books, even if they aren't blockbusters (and most books aren't). Good article on them from the NYTimes (from a few years ago).
I'm published with The Permanent Press. It's run by Martin and Judith Shepard, who are a class act all the way. They're on the MWA and ITW approved lists, pay an advance, are generous with subsidiary rights and royalties, and are extremely supportive of their writers. I've never heard of a small press that did as much or was as respected. On the strength of their reputation, the first book in my private detective series was reviewed by Booklist, PW, Library Journal, and Kirkus and was reviewed in Mystery Scene and Suspense magazines. They've garnered a ton of awards over the years; in fact, one of the 2011 authors, Len Rosen, was recently shortlisted for the Edgar award. (We don't know yet if he'll win it, but he did write a terrific book.)
I can't say enough good things about The Permanent Press and the Shepards.
Judith sent a rejection. She said her husband liked the manuscript and sent to her to read. However, she said it didn't "engage" her enough....
Response was good and professional. I'll submit to them again in the future. My only "gripe" is having to submit hard copies. In this day and age, it seems e-submissions would be the norm for every publisher, but that's just my humble opinion. I initially sent the first 25 pages, then the full manuscript. Roughly 350 pages to a land fill.