I do most targeted searching with ITA, using specific search coding. I use interpretations of Yahoo's dream maps, developed by some FT'ers, to map trends. I use Expedia for multi-city routings, which is how I generally work any trip, regardless of it being a round trip or not. I use ExpertFlyer for specific access to GDS information (like the fares I posted above). I've found some promise with Kayak's new "buzz" alert service, but haven't used it enough yet to comment. I have not used Sidestep, but have heard good things about it. Of course, the airline travel library, FlyerTalk, is searched and monitored daily.
Having said all that, the best deals come right off the airline sites, IME, as I can often target fare buckets which aren't listed yet (or at all) on the wider GDS. I fly mainly UA and the vagaries of their online booking engine are well known. It does offer some interesting deals, once one knows how to properly manipulate it
Currently, when someone asks "Pat, can you find me a good deal?", I first go to ExpertFlyer to pull up all the fare buckets, then target the desired ones on ITA, then plug in the relevant flight numbers on the airline booking engine and peruse their fare buckets/availability as a comparison. I usually use Orbitz (which uses ITA) and Expedia as control checks. I establish a baseline, and check for movement from the competition (too complex to outline here) to help predict trends or near-term responses. I check their routings on FlyerTalk, to see if mileage runners have any opinion. I then advise the person to book or wait, based on my instincts and historical experience. If I tell them to book, I mean immediately, like this minute.
I liken this process to alchemy
Another phrase I use often is "Success is where preparation and opportunity meet". Preparation is what makes one cognizant of opportunity. It's really the same process that is discussed on TUG regarding timesharing, IMO. There's no "secret recipe". It's just a lot of hard work, which I (and others) happen to enjoy.
Pat