The ones we normally check first are
http://www.travelsupermarket.com/c/cheap-flights/
http://www.skyscanner.net/
http://www.travelrepublic.co.uk/

Or try Money Saving Expert for general advice on booking flights;
http://www.moneysavingexpert.com/travel/cheap-flights

Others

http://www.flythomascook.com/
http://www.jet2.com/
http://www.easyjet.com/asp/en/book/index.asp?lang=en
http://www.cosmos-holidays.co.uk/
http://www.firstchoice.co.uk/flights/
http://www.goingplaces.co.uk/
http://www.mytravel.com/
http://www.avro.co.uk/
http://www.flypgs.com/en/
http://www.thomsonfly.com/en/
http://www.thy.com/en-UK/index.aspx
http://www.britishairways.com/