Maruzen bookstore in Tokyo is really great. When I was living in Japan (from 2004 to 2007) I used to visited every weekend. It has a good selection of books and magazines and it is very confortable because you have good spaces to walk around. And it is completed by the kindness of Japanese people who take care of you. And garantee that the enviroment is very confortable.
Maruzen in Marunouchi has an excellent foreign language book section, according to Tokyo standards at least. It's on the 4F floor, and not carefully marked. About half of the space is devoted to art books - for some reason half of any English book store in this city is large volumes of art or pictorial John Lennon biographies - no, I don't know why. The other half is divided into a sizable English magazine collection (Economist is 1,110 yen, Newseek 800 yen), English books, and two smaller German and French sections. Quite a few French audiobooks, for those inclined.
Most of the English books are contemporary paperbacks, obviously intended for airplane trips. However, they have several shelves of the Penguin classics series, so you'll probably be able to find something you like. I picked up a Nick Hornby novel and have been very happy with it.
Maruzen is strictly for buying. I missed the Barnes & Noble chairs and couches. If you want to sit while you are reading at Maruzen, I'm afraid you have to buy your books and walk over to the cafe on the same floor.