I use kayak.com. Please note that the discount airlines such as Southwest are not on there, but Jet Blue is. You still have to go on their airlines to get prices. Good luck.
You can search multiple airports at the same time.
You can search for the lowest prices in a 30 day period.
In the search results, you can look at the prices by airline, by airport, or by time of day.
I've used a lot of search engines and I think this one is the best.
EDIT: But just like a lot of the other search sites, some of the discount carriers are not included, like Southwest.
You might also want to try sidestep.com. It's similar to kayak, but I'm pretty sure SW is on there. I've had some bad experiences with kayak - on a number of occasions, when I tried to purchase a fare, the fare class listed was already sold out, and I kept on having to search again, and ignore the fares that I knew were wrong. Kind of a PITA.
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