What I really want Hipmunk to integrate is low-cost carriers, like Southwest.

If I want to book a flight from NRT to SFO, it's often cheaper to fly through LAX, but the big carriers don't offer that many runs between LAX and SFO. Southwest, on the other hand, has a plane every few hours, and they're really good about rescheduling should I get stuck at customs for an insane amount of time (which is a given, because LAX).