(not a flightfox user but my 2 cents)

Booking an award trip can be much harder to do unless you have an easy route like a domestic non-stop. The ITA matrix won't show you those flights, expertflyer.com used to be really useful but right now you can't get access to the United (and most of *A) data, some airlines have vague routing rules that may or may not play in your favor depending on which agent you talk to on the phone (looking at you US Airways), etc.

I think 99$ is steal.