Fares are constantly being loaded into the system.

But if you're looking for deals from one of the top 50 heavily traveled cities, check out http://www.air-fare.com. I go there every day to see what the latest fares are between my hometown and frequently-travelled city pairs.

Also, after a while on FT, you'll get to know which cities are cheapest to do mileage runs are. For example, PDX to MHT, PVD, BWI, EWR and CHM are often really really cheap and don't require a 1-day minimum stay.