You don't really have a control group to know that skyscanner consistently provides the best results. It's possible that you were happy with your skyscanner experience and believe that you got the best deal, while there was an alternative that would have been much better for you. Flightfox is a relatively cheap insurance policy against that.
I tried it out and the winner quoted me an incorrect itinerary cost -- didn't notice that the airline's quoted price did not include airline fees and taxes (which are in the hundreds of $$ for international flights). In the end, the true winner beat skyscanner by less than the cost of the contest.
Honestly, I find skyscanner amazing; it is the only system I know that finds airline consolidators (well flightfox does of course too) - and has a very easy to use tweaking interface.
http://www.skyscanner.net/flights/lond/berl/1302/1302
There are definitely challenges in gathering & displaying a combination of budget and 'traditional' carrier fares, but to say that either set isn't available via flight search isn't accurate