This seems to be a commoditizing business. Most internet travel agencies offer hotel reservations also, and if you do a websearch, you'll find hundreds of hotel reservation agencies.
We like to use a two-part strategy: Check with some of the
discount vendors for "steals," but if we don't see
something really good, shop the comprehensive vendors for the
best flight for our needs (convenience, air miles, travel time,
etc.).
Airtech has special deals and standby flight passes.
Biztravel targets frequent business travellers, with news features and emphasis on accumulating frequent-travel miles.
Cheap Tickets is a consolidator, and has good deals—if they are available for your flight.
Expedia has probably the most comprensive and flexible site out there. It has an excellent selection of flights, but you can sometimes get a better deal elsewhere.