There is always http://hipmunk.com, which I think has the best UX of any of them (although maybe it is lacking some features, but none I would use anyhow).
I'd recommend www.skyscanner.net, at least for the European users.
Sure, they lack simplistic interfaces of Hipmunk or Kayak but when it comes to actually finding the cheapest tickets and best connections on the old contintent low fare airlines market they're, IMHO, the most reliable.
I'm a big fan of skyscanner. Being able to ask questions like 'what are the cheapest flight from my local airport over this weekend' make for fun trip planning.
I've found Google Flights[1] to be a much better experience than either. It is stupid fast and has a great interface for comparing prices if dates are flexible.
Hipmunk looks interesting, haven't seen it before. Minimalist is the way to go, I think. Can't stand busy travel sites that try to be everything to everyone.
To compare prices between three airports in the same metro, couldn't you use the "include nearby airports" function and just look at the filter list and see the lowest price from each? Just wondering if you've tried that vs. running 3 different searches.
Edit: Doh, fixed the link!