If you find one not on this list, feel free to post about it on the comm, and please tag it "store link". I will then add it to this post. Please do not tag timed ebay auctions this way, however an ebay store's Fullmetal Alchemist category would qualify for posting.
You are welcome to comment to this post with any criticism or commentary regarding any of these stores, and your comments may be added to the post itself. Please put the store name into your subject.
Ideal 808 - Good selection of packs, booster boxes, and starter decks
Atamaii - Some harder to find stuff, prices could be better.
Cardhaus - Good prices on packs of some sets.
Madoka Anime - Another good source for Japanese packs and starters, you have to make sure you're viewing in American dollars instead of New Taiwanese.
Armada Anime - Lots of single cards.