Forbidden Planet London is now in Shaftesbury Avenue. It's got a pretty decent SF & F section, including both the Masterworks series, and some US imports, though the horror section is a bit disappointing (too much King and Koonzt, which you can find anywhere). There are also a couple of shelves devoted to Manga and graphic novels, and a fairly large DVD collection of cult films.
If you're into second hand or remainder books, there are tons of great shops in the Charing Cross Road: Bookends, Lovejoys, Henry Pordes, Any Amount, Quinto's, plus a number of specialist stores like Murder One (crime fiction and thrillers). There's another (better) Quinto's opposite the British Museum, and a couple of occult stores in the general area. Hunt around. Also check out the Waterstones in Piccadilly for a pretty cool horror and SF section (2nd floor).
Then there's Judd's in Marchmont Street, which is pretty good for general fiction. And nearby, Skoob in the Brunswick Center. I've found some pretty good bargains there.
Holloway Road has the Fantasy Center which I occasionally pop in to. Their books are a little overpriced in my opinion, but they have an enormous selection of stuff, including a lot of hard-to-find books (be prepared to pay through the teeth for these though).
What else? Oh, yeah, Foyles of course. It's OK for SF, but their general fiction section is bind-bogglingly massive, and some of the best fantasy can be found there (Borges, Cortazar, Davenport, Kis, etc), plus they've got a totally groovesome Jazz cafe to while away the hours in.