Junkudo will let you select books, place orders for things not in stock, and designate a branch for pickup and payment. This is a great way to plan ahead for hard to locate books/issues of journals and not waste time looking for things you already know you need. Depending on the amount they will deliver to you home/hotel.
There are a few booksellers who will take credit cards, but many still will not. They will take bank transfers or postal transfers (i.e. good if you are in Japan, but not if you are overseas).
