I'll always have a soft spot for Foyles, but I loved Murder One, the mystery / crime bookshop on Charing Cross Road as well, not sure if it's still there. There used to be one I went to all the time on Holloway Road, inside the shopping centre there, but I don't know if it's still there either. I think it was called Titles. There were some great outlet / second hand bookshops up Charing Cross Road as well. Used to just walk up there after work going into shop after shop.
A new one opened in Glasgow near my old house that was quite good but very expensive, styled itself an 'antiquarian bookshop' rather than second hand, Young's Interesting Books on Skirving Street, but they did have some good stuff.
Here, my favourites are the Academia Bookshop and Neopalace Luxor on Wenceslas Square, Charles University bookshop, and a little English language one called 'Big Ben's' up the back of the Old Town Square. Neopalace has more stuff, I think, but Academia gives me 10% discount because I have an Opencard, and is a bit more dusty and, well, academic feeling!