Aah, the penny drops. (Hipmunk site was top of reddit a few days back). It looks great, but it would be amazing if they could incorporate Ryanair, Easyjet, Fueling and German Wings.
A ton of people request this. We're working on it.
I would also add Southwest to that list. The reason I don't use sites like Orbitz, Travelocity, etc... isn't because they are hard to use it's because Southwest is nearly always the cheapest and they don't jerk you around. I once bought a flight on Continential over Southwest to save literally 4 dollars. I've never been so sorry about a purchasing decision in my life. Long story short Continential was so bad I never actually made it onto their flight I ended up booking a Southwest flight instead. After that I don't even check any sites except Southwest.com anymore for domestic travel.
But from what little I know, you also aren't allowed to list Southwest prices on other online booking aggregators. Our company travel site makes us open their site separately to check prices for this reason (I think -- it seems highly unlikely to be a technical incompatibility).
Hmm. I have really complicated itineraries and so far it looks like ITA's matrix search only not as flexible/powerful. It has potential, though.
I wrote my own client-side multi-flight planning app about four years ago, using web scraping to include Ryanair, Easyjet and others, in order to plan a cheap vacation. A particular problem with Ryanair is, I believe, that they are explicitly against any kind of disintermediation or technology-enabled price competition.
You cannot scrape their prices because they keep bumping them by a cent for each N tickets (so they can say that "only N seats left for X euro, book now before it's too late" all the time), and also because you cannot reliably reverse engineer all their random fees.
Actually, I can scrape the prices, because it was my personal client, only ever run by me, with fresh prices confirmed by faking a run through the booking process.
www.skyscanner.com includes Ryanair and other cheap airlines. At least at some point they did :)