If you don't mind travelling by train, Amtrak is pretty good, and if you're making a lot of journeys within a month or so, you could get a pass. All your travel for $600 ($1000 including Canada). (They have fifteen day ones for the US as well, $500.)
For flights though, Expedia's all I've got, too. If you keep checking, though, they add cheaper seats sometimes. I saved $50 by waiting a couple days to book my Portland --> LA flight.
I always book my flights through Orbitz.com, although I don't know how they do for multi-destination trips.
Dex is right about booking with the airline, that's usually cheaper and involves less fees.
I use Sidestep (http://www.sidestep.com/
) to find flights, then double check with the actual airline to be sure I'm getting the best flight information. That's how I did my Japan travel.
Also, Travelocity. And inside the US, depending on where you're going, jetblue and southwest.
However, if Ben asks, I didn't suggest southwest.
Omaha is not on Kate's itinerary.