Did you try Hotwire.com? If you're flexible on the times of day you fly, you can sometimes find great deals. The basic premise is that you say what days you want to fly from one city to another (and how many stops) and then they show you various itineraries with prices. You buy the flight and then you find out the time of day the flight is after purchase.
It sounds random, but the site is totally legitimate, and you can get some GREAT deals. I also really like travelzoo.com for hotel deals, if it helps. You can subscribe to their e-mails.
Good luck,
Angie