Most definitely Kayak - it's my number one stop for flights, be they a year ahead, or 5 hours from now. And they certainly support LCCs - I once used Kayak to work out that Miami to London was quite a bit more expensive than Miami to Dusseldorf, and find another way for the final leg. So I flew to Dusseldorf, trained to Cologne, went into a net cafe, found an EasyJet flight later that day, had lunch and headed to the airport.
It's certainly made travel more flexible for me - thinking back to using travel agents makes me cringe :/