Does anyone know of any websites that sell Japanese books cheap? The Japanese Amazon site is way too expensive due to shipping, so I'm looking for a cheaper alternative.
Kinokuniya has some US stores. Barring that, your best bet would be to check out the Amazon Japan thread on here and get set up so you can buy digital books.
yesasia.com is popular. I've bought from them a few times and their prices are reasonable but the shipping takes kinda long. If you're looking to buy a bunch of stuff you can get free shipping if the total is over forty bucks or something.
edit: just a word of caution. if you do buy from yesasia make sure to double check that the books you're gonna get are actually in Japanese because plenty of people on here have been burned, accidentally buying Chinese books.
I've ordered from honto.jp a few times. I think their pricing is about as low as it gets and they don't add sales tax for international orders. You can choose the shipping service and they will charge you the actual shipping cost. The cheapest option is SAL Economy Airmail; their prices are based on weight (it's not exactly cheap but not Amazon-like ridiculous either). With SAL I usually receive the goods about three weeks after ordering (though it can vary quite a bit, I suppose it also depends on where you live).
honto.jp also have a seamail shipping method which is even cheaper than SAL, if you're willing to wait a month or two for your books. That's what I use; if you buy a big pile of books then you have a backlog to get through while you wait for the next set to arrive...
if you really live in philadelphia you could check out book-off in NYC. they have one dollar section, two dollar section, and more expensive section. also they have a one dollar section for manga.
the one dollar section does have goood stuff but just you gotta fish it out from all the crap.
I love honto.jp. Really difficult to find cheaper prices or shipping! I order magazines and sometimes books from them about once monthly. Shipping SAL it usually takes about a month to arrive, but I've had things show up in as little as two weeks.
If what you are looking for is popular (manga especially), you can find it on the US ebay site for okay prices. I've seen full runs of some manga series used for much cheaper than buying single volumes. Novel selection is more iffy, but I just got all three volumes of Murakami's The Wind-Up Bird Chronicle for $5 two days ago. Handy if you don't want to wait for overseas shopping.
The Book-Off in NYC is also fun if you aren't set on buying something specific.