The ultimate travel geek toolbox:

http://matrix.itasoftware.com - especially once you learn the advanced QPX language, e.g.:

    SFO,LAX CX,AA,KE F HKG,ICN,NRT ~CZ+ KMG

Search for flights from LAX or SFO, on Cathay Pacific, American, or Korean Air, a single flight to stopover cities Hong Kong, Seoul, or Tokyo, then any number of flights except on China Southern to Kunming, China (where I happen to live).

They're also the source of inspiration for Hipmunk's Time Bar interface.

The one downside: you can't book directly through them. But once you know your exact itinerary you can go book somewhere else. Sometimes you'll have to call to get the fare code/construction that Matrix recommends, as it won't always come up in an airline website or kayak search.

http://kvstool.com/ (Subscription required, windows/WINE) Search all kinds of fare, routing, timetable, award info. Uses the Sabre, Amadeus, and Worldspan (the 3 major info brokers). Has a pretty decent mobile website that has saved my ass more than once (I can see that there's open seats in business on a particular flight, etc).

And down the rabbit hole: http://flyertalk.com/

Lots of people also like http://expertflyer.com/ (subscription required) as a web-based alternative to KVSTool, but I find its search engine too restrictive and the results more difficult to quickly parse.