A Note on Bookstores
Both Borders and Barnes & Noble carry books on Japanese (look near the reference section) but the selection can be limited and swamped with low quality "Learn Japanese in x days/ x minutes a day!" type stuff. Do take a look at your local bookstore though, since you can actually look through the books.
Online Stores
Amazon.com has a great selection, and the bountiful reviews are extremely useful. Basically anything published in the US can be found here (not sure about other countries), but again, vague search terms like "learn Japanese" will also pick up a lot of non-serious stuff (read: "won't actually get you anywhere"). The key to finding the real gems is to get to a decent item then find the "other customers viewed/bought" section.
The Japan Shop seems to be a good place to find textbooks and the like, including books that are imported rather than properly published in English speaking countries. I haven't examined them thoroughly enough to comment on pricing.
White Rabbit Japan specializes in books and other items that are hard to find outside of Japan, including listening comprehension workbooks and JLPT prep material. They also publish a series of Kanji (and Kana) flashcards, which are sold on Amazon as well.