MANGA STORESBuy.com- Go to Buy.com for the cheapest
licensed (English) manga. Right now you can only pre-order up to Volume 5. The manga's currently being licensed by TokyoPop.
Kinokuniya- This is a store carrying manga, books, magazines and such. If you can find one near your residence, I suggest going there instead of ordering online. ^^
Planet Anime- Also a store, with a rather large collection of merchandise, manga, books, music, etc.
Japan Manga- This place has some of the rarest selections in stock. O_O You can also find doujinshi, CDs, VHS, and merchandise here. But there are quite a few hentai manga too...
JPQueen- I love this place. It's got the cheapest of of the cheap manga, artbooks, doujinshi and CDs for a decent quality, AND they have all the rare stuff, all imported from Japan. What's not to like? XD
Aestheticism Cybershoppe- Lots of manga, doujinshi, magazines, and such. They have a pretty large selection and at relatively reasonably prices too.
BOOK STORESSasuga Books- Very good selection of artbooks, magazines, DVDs, videos and more. You can also find manga here, great service too. :) Everything's imported directly from Japan, and you can place special orders.
DVDs/CDs/VHS/OAVs STORESCD JapanVery nice place with a ton of different CDs, VHS, and DVDs of all different kinds of anime, J-pop, J-rock, movies, and more.
ChibiTokyoMost of the Gravitation CDs can be found here, for an ok price. No sound stories or anything else though. Still, I'd go just for the soundtracks.
AnimeToxicAgain, most of the CDs can be found here, including the sound stories, for a pretty cheap price. They also have DVDs.
AnimaxisThe
only store I know of that sells the Gravitation OAVs. It's not cheap -.- but if you're desperately looking for OAVs, this site has them in DVD format.
MERCHANDISE STORESPlanet Anime- A nice store with a large collection of merchandise, manga, books, etc.
U.S. Anime- Great variety of merchandise, phone cards, clearfiles, doujinshi, etc.
Also check out EBay.com for auctioned merchandise.