Human intelligence/Paranoia. I don't allow myself to get one in the first place or know enough about how your computer works to know that a change made to your system wasn't done with your permission. Or, if you do permit it, that the changes aren't doing anything that will hurt your system.
Running a program like zsoft uninstaller before and after installing a new program is one way I track sytem changes.
i also have a virtual computer that I use when i visit questionable websites and install software i don't trust on it first. I can kill it an go back to a previous version easily, or start up another instance of it to try different things.
I also a network traffic monitor to make sure I am not broadcasting unintended information.
I am basically manually doing most of what an antiviru is supposed to be doing. I do use Microsoft's security essentials, but I don't trust any antivirus program to fully protect me.
It can be a pain, but I work in IT, so I kinda have to know this stuff.
MCSE+i NT4.0, MCSE 2000, MCSA 2003. MCITP 2008, MCDST XP/Vista, MCITP Windows7, MCTS, MCP. VMWare VCP3, 4, 5, CompTIA A+, Server+, N+, Security+, HP Service Partner, and a few others I've picked up along the way, like Fluke CCTT and other vendor specific certifications.
I have been working IT since 1998. Now I am a consultant, but my last official title was senior infrastructure systems engineer.