Various Online Manga Stores

American Stores

Sasuga Books :: They are great people, generally quick, and they have a frequent buyer program (gotten several free manga in the past). They do special orders, so if you don't see what you want, just ask them about it.

Planet Anime :: It's a bit more expensive, but another option.  They also do special orders, and at times, they have good sales on in stock items.

Animart :: Probably the cheapest prices in the US and have fast shipping but this is because they don't do backorders. You can only get what they have in stock.
 

Japanese Stores
(shipping *will* be expensive)

Acclimate Solutions :: If you buy used and ship via sea mail, you can potentially save at lot if you order a lot. Just have to whip out the calculator to determine the best method. Also, they don't always pack well, so if you are anal about quality, don't order from them. This is the place where I purchase manga series for the cheap price not caring it'll come a bit bent (i.e. Conan, Devil & Devil).

JPQueen :: They have some great deals on complete manga sets, and much better with shipping than AS, but less of a selection. Good place for more popular manga series.

Animaxis :: Some great prices, but they only ship via EMS, the most expensive alternative. Plus, not a huge selection, although more recent manga.

Other

And while it isn't always the best method, E-bay does have good deals at times. Just be careful to check and see what language it's in (I've gotten a couple Chinese translated manga in the past). Also, never believe people when they say it's a complete set - check that fact for yourself. JPQueen does e-bay as well, but sometimes it's cheaper through their site.

Graphic Novels

I get the original versions of manga, thus I don't know much about graphic novels, a.k.a. English translated manga.  The best suggestion I have for you is to check Barnes & Noble online for a recent listing of available and upcoming graphic novels.  Just go to 'browse books' and then look under the fiction section/graphic novels/manga.