We use http://couponsdealspromos.com For travel(see links to kayak). You can also try Southwest directly.
When I was in the military everything went through SATO travel. It may not even exist anymore. Anyway, they would find the cheapest fights or bus or whatever. Kinda like Orbits or Expedia. The problem was you would fly way out of your way or pass you destination and have to back track (most of the time) and you never got a direct flight unless you were headed to a hot spot.
The other option is if you are in the military to see if you can get a military flight, like in the cargo hold of a C-130 or something.
I suggest that when you go to the travel office, ensure you tell them you are looking for the military discount.
Telling them that information makes their prices search much simpler.
A lot of variations exist, so ensure you tell the office.
I think Continental offers great price. They have a business class that feels like first calss. For what we get, it is cheaper, when compared with others airlines.