Book through the airline
KAYAK, Orbitz, and other travel booking don't charge booking fees to the traveling public, but somebody's still gotta pay that gnome, and that somebody is the airlines. Since the travel site gets a cut of every ticket they sell, the airlines prefer customers who cut out the middle man. In almost every case you can use a travel site to find the best fares, and then go to the airline's site and buy from them directly for the same price. Then, when your reservation pops up to airline agents, it'll show that you booked directly through the airline, and you'll be treated like a loyal customer rather than a bargain-hunting Internet stalker. Even if you totally are.
Check your emails
Another reason to book through the airline: promotional emails. They'll be clutter 90% of the time, but when a flight is overbooked, airlines will email people who booked through them with some pretty aggressive discounts for First Class upgrades. Check your “promotions” folder (or mark the airline's emails as non-promotional) regularly to see if your flight is among those offering them.