We usually did SpaceA when we were active duty... but if you don't have time/patience to hang out in an airport for 1-2 days...
The Travel Specialist on base... I've gotten rates at 25% of what they go for to the public
Travel Agent off base... Again, ot as good as military travel, but decent at 50-75% of normal 'deal' fares (do your research ahead of time for the cheapest you can book for).
www.travelzoo.com they have a top20 which is pretty phenom
Double tickets. AKA say Hawaii to Seattle or San Fransisco, or LA, & then a "short" flight and then a deal fare from SEA or SFO or LAX to where you want to go. Different than "connecting flights", it means you can snag say 2 round trip tickets from LAX to NY (or wherever) for $100 each, and save $500 on using the same airline. Trick is to find cheapest to fly TO and cheapest to fly OUT of. AKA, LAX is almost always 'better' than SEA.