http://matrix.itasoftware.com/
Flight search, owned by Google, searches a month's worth of dates, not quite sure I see the point, but trusted folks rave about it.
http://www.ebookers.de/
Some crazy cheap flights if you get the rights date / destination combo.
http://www.alibabuy.com/
Cheap flight search, in French only, but seems to cover some airlines that SkyScanner didn't. Nathaniel found ultra cheap flight from Marrakesh to Marseille for example.
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.