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.redtag.ca/
RedTag are a cheap flight / holiday search engine. Recommended by Canadians who found uber cheap tickets from Montreal to Belize City.
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!)
http://www.mobissimo.com/
Mobissimo is a travel search enginge. You can search for flights, hotels, etc, etc.
http://www.whichbudget.com/
WhichBudget.com lists all the budget airlines that fly from country to country. You can search by departure and arrival, and they provide links to the various web sites. Damned handy! :)
http://www.jetblueairways.com/
JetBlue are a budget airline that operate across most of the US.