Homeland Security said on Thursday that it performed approximately 1,000 laptop searches from October 1, 2008 through August 11, 2009. One way to protect yourself from these searches is to use whole-disk encryption from a company like PGP and make sure your laptop is completely powered down when crossing the border.
This will stop them from seeing your files but it won't stop them from holding onto your machine. If you must travel, you might want to look at using VPN technology on a cheapo netbook (along with running CCleaner and Eraser at military-grade shred-level.) If they hang onto your machine for longer than it takes to open it and verify that it's a computer and not a munition storage device, the chances are good that they'll break it for you when they realize that you haven't left them anything to look at. Having that capability routinely in place may go along way toward proving that you were framed if they decide to put a present on your machine and then arrest you. It should be clear to everyone that searching people's electronic devices at the border has no positive effect on anyone's security because the whole process is completely circumventable, and only serves as security theater with the added benefit to the ego-challenged of making it easy to victimize innocent people. Anyone that supports this kind of thing needs to be returned to the private sector.