When a friend of mine needed to rent a London flat for a study abroad semester, she used 2 different sites. One was www.rightmove.co.uk - she liked this one because of a feature called "Draw-A-Search." It allows you to show on a map the area you want to search in, and then it shows you available flats in that area. The other one she used for research was www.findaproperty.com. One piece of advice: she ended up using a leasing agent in London and said that was better than the online sites, so you might want to keep that option in mind.
www.zoopla.co.uk is very well laid out and nice to use. It mostly has flats on the higher end of the market though. Gumtree and Loot have a lot of cheaper rooms/flats for rent, or go to a high street letting agent wherever you're interested in (I would _disrecommend_ Foxtons though, I found them to be super expensive for what you get)