Here is a different kind of independent bookshop - housed in a glasshouse, the Wapping Project Bookshop specialises in art, photography and new fiction. On Thursday evenings the tiny place hosts poetry readings, book presentations etc. It is part of the Wapping Project (check it out here), which apart from art exhibitions etc also has a nice restaurant, so you can make it a real outing should you live quite far away.
If Wapping is too far out of your way however they have relocated from today to fashion shop COS on Regent Street for 2 weeks. Less charming, though, but probably warmer to take your time and browse a bit.