PCAS - Pasadena Cartoon and Anime Society

Robert's Anime Corner Store -
Media OCD - sell titles released by AnimEigo, Whole Grain Pictures, and Discotek. Founded and owned by Justin Sevaki (founder of Anime News Network), who bought AnimEigo from its founder Robert Woodhead (also the co-creator of the Wizardry game series).
Sentai Filmworks - they only sell the titles they publish, but this allows them to hold sales all the time and mark down discounted items to their wholesale price (or much lower for items which have been in stock a bit too long). Sentai is kind of another name for/imprint of HiDive.
Diabolik DVD -
All the Anime - UK online anime store for UK publisher Anime Limited. They seem to have some sort of cross-licensing arrangements with various US publishers (so if the only US release of a title is a very expensive set, they might have a less-expensive version available, assuming you're OK with Region B Blu-rays). They also pick up the occasional title which isn't and never has been license in the US.
Media Blasters
Crunchyroll Store
Amazon

Pasadena Cartoon and Anime Society