I have been using Yapta for quite a while, but don't hear much on this forum about it. Its search engine is based on Kayak, and you can track a flight for price changes. Yapta will email an alert when the price dropped by certain amount.
The fares listed on Yapta is bookable on the airlines website directly via a link most of the time, though the more obvious links provided are to 3rd party sites. So far I find the prices are as accurate as on the airlines websites.
Yapta also have a refund feature that if the price of the ticket you purchased dropped by certain amount, they will help you to make a claim. I have not used this feature before but I think in order for Yapta to do that, they have to be able to receive accurate fares information from the airline on the fly!
Try it at http://www.yapta.com/
I also use Skyscanner to search but always book directly with airlines, difference with Skyscanner is you can't do multicity search, and they usually direct you to book on 3rd party sites which I would avoid.