Tokyo residents who are shopping for used English books are likely familiar with "Good Day Books." The shop has been around for about 15 years and has a good selection and decent prices. They will order new books in addition to selling used books. Used books can be traded in for store credit which can then be used to pay (100%) for used books you purchase in the shop (except for the 5% consumption tax) as well as 20% of the price of new books. We've been trading and buying books there for quite some time now and we tend to get 30%-50% of the value of books (closer to 50%) in credit.
Recently, I came across a link to another used book shop called "The Blue Parrot". Since this shop is in Takadanobaba and Good Day Books is in Ebisu (both on the Yamanote line), my husband decided to take a bag of 18 books to both shops and see which gave him the better deal and offered the better shopping experience. Since he has a lot of experience with Good Day Books, he pretty much knows what he would get for the books and which books they were likely to accept and which they'd likely reject so he went to the Blue Parrot first.
The 18 books he took were a mixture of novels, humor books, and a few non-fiction books including one on baseball, a large book on MYST/Riven (the development of the video games) and a few New Age philosophy books. The Blue Parrot agreed to take all of the books and would either pay ¥960 or give ¥2,200 of credit which could be used to buy used books.
The shop itself was relatively small and narrow. There were audio books on CD. They carried Stephen Fry's audio versions of Harry Potter novels, for instance, but they were relatively pricey (¥12,000 each). The books were pretty well-organized and one could likely find a book one was looking for if it was in stock. They also carry DVDs of movies though my husband thought most of them were relatively low-priced unpopular titles (around ¥700 each). There were exceptions though. Babylon 5 season 1 on DVD was available used for ¥3,000. If you buy DVDs there, you have to take a good look at formats and region codes though since some of the discs are PAL. The web site for the shop mentions that they also carry CDs but my husband didn't see any.
My husband passed up on selling or trading in books at The Blue Parrot because he was sure he could do better at Good Day Books. Good Day Books refused 4 of the 18 books he took back (the MYST/Riven book, 2 humor books, and Dragonflight) but still gave him ¥5,200 in credit. So, he got more than twice as much credit for 4 fewer books at Good Day Books. The Good Day Books shop is at least twice as big as The Blue Parrot and more comfortable to walk around in and carries a larger selection.
In terms of the advantages for each particular shop, The Blue Parrot offers on-line shopping though the selection doesn't seem very good at this time. When I did a search on "humor" via the on-line shop, no results came up and other types had limited selections. I'm guessing the selection will improve with time. Also, The Blue Parrot carries DVDs and Good Day Books does not. Finally, if you are leaving Japan forever and have no use for store credit, it's better to get a small amount of cash for your books from The Blue Parrot if you are unwilling to go to the trouble of trying to sell them yourself via free ads in publications like Metropolis. Good Day Books doesn't offer cash for your books. If you are remaining in Japan, you're likely better off taking your books to Good Day Books because you get a great deal more credit to apply to future purchases and a larger store to use that credit in.
My husband said he wouldn't make a return trip to The Blue Parrot unless he was thinking of paying cash only for books because of how low the trade in credit he was offered was going to be.