The Wall Street Journal does a summary of new airfare comparison sites. None of these sites actually lets you buy the ticket -- they search through large databases to point you to the best place to buy.
Farecast.com is one I've used since it was in Beta. The UW professor who made the site got started by reverse-engineering the pricing strategies of airlines like Alaska, and now the site tries to predict how prices will go up and down over the next few weeks and months. So far it's limited to flights out of Seattle or Boston.
Farecompare.com looks similar, though it uses historical info.
Here's the WSJ's sample of how Farecast did: