ITA Software's beta tool is more flexible than any other fare search engine I know of. It can handle pretty much any search you can dream up, as long as the dates are fixed plus or minus one day. You can't purchase directly from them, though it will display the fare basis and booking class and you can then go to another site or a travel agent. I think it also lacks access to at least some webfares.
http://www.itasoftware.com/ and click on the "Search for Airfares." Free registration is required on the first use.
For example, for a trip on AS from SEA to one of LAX, SFO, or OAK, one would enter:
Code:
From: SEA :: AS+
To: LAX;SFO;OAK
(":: AS+" means one or more flights on AS). You can sort the results by airline, destination airport, or time of travel. For more about specifying advanced searches, click "Show Advanced Options" on the search page, and a very small link will appear offering help.