http://www.hipmunk.com/
Search flights and see them laid out in a grid that shows take off time, layover time, stops, and sorts according to "agony" which tries to factor price, layovers, etc.
http://www.orbitz.com/
Orbitz is a travel search engine like Kayak.com. I think they handle booking, which makes them much more reliable than Kayak who simply advertise fares.
http://www.budgetlonghaul.com/
Budget Long Haul is a web site dedicated to flying budget around the world. It's run by the same guy as WorkingNomad.com (I think!)