This page will eventually contain a very long list, so it will perpetually be updated as I gather more information. Some of these are associations for booksellers as well as publishing houses.
IOBA (Independent Booksellers Association)
The Pushcart Prize (not actually a publisher, but a very prestigious award given to writers whose work has already appeared in a small press. The kind of award that attracts attention)
Amazon.com link for booksellers (if you already have a book you want to sell)
Barnes & Noble.com link for booksellers (same here)