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.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.ebookers.de/
Some crazy cheap flights if you get the rights date / destination combo.
http://www.flightstats.com/go/FlightStatus/flightStatusByAirport.do?airportCode=CPT
Live flight arrivals from flightstats.com for Cape Town (CPT) airport.
http://www.jetblueairways.com/
JetBlue are a budget airline that operate across most of the US.
http://www.kayak.com/
Kayak allows you to search multiple flight / holiday web sites and filter the results using some very cool ajax.
http://www.mobissimo.com/
Mobissimo is a travel search enginge. You can search for flights, hotels, etc, 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.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.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! :)