I generally just go to the airlines websites and do the research myself. I have used expedia and found it to be expensive. Have you seen this one:
Budget Airline FlightChecker tells you when to go for the cheapest price: MoneySavingExpert.com
The notice at the bottom made me laugh

- "Ryanair are currently having problems with their website". It should read that Ryanair are suing the companies that screen scrape -
Ryanair wins German court victory in screen-scraping injunction | The Register