I like abebooks.com for used/discounted books, including manga. (They're owned by Amazon now, if that makes a difference to you.)

Also this list might be helpful ( #11 is pretty nifty! ): http://www.lifehack.org/articles/money/15-best-online-bookstores-for-cheap-new-and-used-books.html

Goodreads (dot com) - if you are looking for a specific (Manga) copy they will direct you to other online stores.

Their online stores (links) to get a copy of Orange (Complete Season 2) was:
1) Amazon
2) Audible 
3) Barnes & Noble
4) KoBo 
5) Appke iBooks 
6) Gogglr Play 
7) Abebooks 
8) Book Depository 
9) Indigo 
10) Half,com 
11) Alibris 
12) Better Workd Books 
13) Indie Bound 
14) Libaries 

When I looked for a different Manga (Tokyo Ghoul #5) I got the same online listing. 

I've used Valorie Books - they also link you up with other sources for used Manga - prices are like Amazon with 1 cent books and $3.99 S/H and up.

Know of, never used - Anime Cornerstore (dot) - new Mangas 
Kinokunia Books - English, Japanese and Chinese Mangas and books. - no used just new w/new prices.

Weluma (dot com) - out of Singapore 

 - they offer discounts and sell complete sets at very good prices. Including what I call "Grab Bags (or Grab Boxes) of assorted Manga - one offer was 25 assorted Japanes Laungage Mangas for $49.49 and free shipping, another was 38 Japanes Soft Cover Comics for $39.99, they had 100 pages w-28 offers per page just for discounted deals being offered - worth checking out if only for a visual history of Manga made but no longer readily available - they had "one of" copies in 3 figures, as well as 1st editions for $2...they have complete editions as well as single pieces. I'd be very careful about using any type of charge cards w/overseas purchases - just saying.


There are of course several thousand places to buy new and used Manga's -

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Good luck Yuki!  
 

Hmmmm.... 

Out of the list that Danny N. gave you, I'd say to start with betterworldbooks dot com. 

If you go there and hunt through their bargain bin books and pick at least 5, they go from being $3.99 each, to $2.50 each. (which is cheaper than Amazon at .01 cent and $3.99 shipping each) The only thing to keep in mind, is that don't always rate their books very well and some can be more beat up than they should. Plus, they can be a pain in the butt with returns. Still, for the price, I go back. 

I get a lot of deals on Bookoutlet.com

I'll put a plug for our local used bookstore (who does sell online):

http://www.janeaddamsbooks.com/

She usually has several shelves of manga/comics and they change frequently, so appears to be a steady supply coming into the shop.