Airlines are hurting badly. Ever hear this old joke? "What's a good way to become a millionaire? Invest a billion in an airline!"
With the U.S. dollar doing as badly as it is and the way airlines generally lose money as a business, they're looking for any possible way to cut their losses. Since the airline industry loses far more money than it takes in, many airlines are looking to merge, which could be a good or bad thing (although probably mostly bad). Currently, the airlines do as little as possible for the passenger and there are many competitors -- if the market shrinks and these airlines know Americans have little choice in choosing who to fly with, they'll raise prices, lower service and care even less about their passengers than they do now (if anyone could imagine that's possible).
What I've found the best thing to do (aside from what Kathryn did) is to sometimes take different flights on multiple airlines. That sounds counter-intuitive and it's often much more complex, but sometimes it's easier and less expensive overall. It depends on the airline, bags (whether or not you're checking anything) route, travel date (time and day) and airport, since an airline's hub will offer more flights, but also be far more crowded for that particular airline. IAH (Houston, TX) for instance, is Continental Airline's main hub and there have been times where the lineup to check-in and go through security at Termina C (which is reserved solely for Continental) has been backed up so far, it's gone outside and wrapped around the building, as if people were waiting to get into a nightclub.
One time, I found it worked out better in terms of both time and money to take a combined Continental/WestJet flight, instead of flying Continental all the way, using another U.S. airline in addition to or instead of Continental, or even Air Canada. It was a lot of work to figure out the schedule, but in the end, it was worth it.
Oh... and one quick note: even though United Airlines is partnered with Air Canada, you can only check-in online with United if you're within the United States. Otherwise, you have to check-in at the airport. I've never had that problem with Northwest or Continental; I can't speak about Delta or any of the others, since I haven't flown on them to or from Canada. Honestly, I think Air Canada is the best airline to fly with regarding Canada. Then again, I'm biased, since I really like their personal video screens (which is something I've never seen on any economy flight with a U.S. airline).