Forbidden Planet
Foyles - and on the same road are probably 100 second hand/other book shops so it's great for wandering and having a nosey.
Gosh! Comics
The Waterstones at Oxford St Plaza isn't huge but is definitely worth a stop in as a lovely giant lady who frequented wotmania works there and looks after the Fantasy/Science Fiction/Crime bits and is very good at recommendations, as well as of course general enthusiasm for all things geek.
Not so much with the fantasy and comics, but a quick pop into Daunt Books Marylebone is worthwhile if you're in the area just for the building - especially the travel section at the back right of the shop. It's neat.
For some independent offerings, this map looks useful. If you're around North London, Big Green Books is a lovely place with some really good events.
I'll let you know if I think of any others
*MySmiley*