Good article over at Linux.com about how to secure your Linux laptop from a physical and data perspective (including hard disk encryption). I usually see a ton of articles about how to secure Windows and Mac laptops but not a lot on Linux. From the article:

"There are three problems with having a computer stolen: the loss of the machine, the loss of the information on it, and the possible security breach if that information includes sensitive information or client data. Each of those problems requires a different approach."

The author talks about several different solutions around whole disk, separate partition, and USB encryption using solutions like dm-crypt and TrueCrypt. I am a personal fan of TrueCrypt and I have been using that to secure my data to a USB drive. There is also some good stuff on laptop tracking solutions for Linux. Don't forget, one of the best deterrents...is to use a cable lock..yes, a cable lock can easily be cut but as a deterrent to physical theft it works pretty well.