I found this site that sells overstock of books and they have a lot of manga for cheap. Most of the manga go for like 2.50 to 3.99 (65 to 75% off).

This is how they explain the discount:
"BookCloseouts.com is one of North America's largest sellers of Bargain Books. Bargain Books are new, unread books that the publisher sells-off in volume to reduce excess inventory. Sometimes the publisher printed too many copies, in other cases bookstores purchased too many copies and have returned them to the publisher for credit. The books therefore have been handled a few times but are still in excellent condition."

Also they do scratch and dent copies too.

Here's the link to the manga section:
http://www.bookcloseouts.com/default.asp?N=3440&Ne=349&org=sub