Honestly, if you don't include the 2nd and 4th largest European airlines[1], you might as well forget about the European market entirely.
Skyscanner and Kayak both include the low-cost carriers.
[1] http://en.wikipedia.org/wiki/List_of_largest_airlines_in_Eur...
Note that sometimes you have to click the "show all" link at the top of the search results to get low-cost airline results to appear. (This is possibly revenue-related.)
This is a large part of my job. We have content from many airlines which are not listed by ITA, Amadeus, or Sabre
Skyscanner shows budget airlines (including both Ryanair and easyJet) along with 'traditional' airlines (BA, KLM, Virgin etc etc). In fact we show almost every airline in the world.
If you are searching for a route which you know Ryanair/easyJet to fly but we are not showing it, please do contact our customer feedback team (http://www.skyscanner.net/contactus.aspx) with the details and we'll investigate immediately.
Thanks
Sam www.Skyscanner.net