They could also have altered the BIOS. Not sure the typical burglar carries around a collection of altered BIOSes, but the only assurance you have of your computer being safe is to completely replace the computer.Quote from Bickz:
if you are truly paranoid about this, then i suggest a full re-install after doing a complete wipe of the hard drive. yes, it's a pain in the butt, but the best assurance you can get. had you pulled your hard drive (without booting up) and had it forensically examined, you would have known whether or not it would have been accessed during your absence.
While nothing will stop someone who has physical access to the computer, you can prevent a lot of things by setting a BIOS or boot password so that they can't boot from CD or USB drive. Opening a computer and plugging the hard drive into another device to write malware to it is fairly time-consuming. I think most intruders want to get in and out in a couple minutes.
You may also want to consider installing a surveillance system with cameras, either one that records locally to tape or hard drive (although they could possibly just steal it) or a webcam. When I was burglarized a few months ago I considered putting up a web cam, but the apartment gets up to 90 degrees during the day during the winter and any computer that was powered on 24x7 wouldn't last too long. (I can't leave any windows open - that's how they got in in the first place.)
