In my case on Flightfox, the person was clearly just using some software. The time investment was probably minutes.
The value for me is that this person knows all of the rules -- cheap legs, good days to fly, how to get X or Y, fare codes, etc. Plus they have the underlying software that powers ticket searching, they don't have to use ridiculously terrible web portals like us normal folk.
In my case, Flightfox took what was a simple round trip "I am flying to Sydney for a conference" for $2400 and turned it into:
* Fly to Sydney
* Return via Manila, stop for a week
* Return via Hong Kong, stop for a few days
* Return to San Francisco
They teased out my layovers into full-fledged stops, and brought the total cost down to $2100. They found a way to get way more value out of this trip than I would have otherwise.
Of course -- then they gave me a pile of fare codes and letters and said "call the airline, good luck!" I haven't actually booked the tickets. :(