Used English books at Blue Parrot and Book-Off book stores
The store is famous among the English speaking and Expat communities because of their fairly large collection of used English books. However, on my visits, I'm always a little disappointed since their books were all somewhat expensive and their selections, from what I noticed, seemed dated. To pay almost close to the original cover price for an edition that has been through numerous publishing cycles since then isn't much of a good deal for me.
If they priced their books cheaper or at least fairly they would move a lot more products off the shelves faster and have more space for newer books.
My usual favorite for English books is the Book-Off book store chain of used books, videos and music.
Although most of their stores (which are located all over Japan) carry an impressive collection, their Shibuya store seems to stock an impressive supply with many current titles. Their selection also seems to be replenished frequently with new books, and their pricing is surprisingly low. I picked up a barely read copy of "An Inconvenient Truth" by Al Gore for 200 yen last year.