Best web sites - well you don't say where the flights are for but assuming they are long haul - I usually use Travelocity.co.uk and compare their prices to Opodo and then to the airlines own website - and book with the one with the best price!
auntiebertie, why dont you try lastminute.com and compare with expedia.co.uk? I find them cheaper than the ones you have mentioned. Then I also compare with the carrier's website. www.airline-network.co.uk is also pretty good!
Another site for cheap flights is http://www.openjet.co.uk/index.jsp. I recently booked flights to Johannesburg and they were the cheapest - albeit the flights are not direct.