How do I protect against rootkits

the book about rootkits http://www.awprofessional.com/title/0321294319
http://research.microsoft.com/rootkit/Strider GhostBuster detects API-hiding rootkits by doing a "cross-view diff" between "the truth" and "the lie". It's not based on a known-bad signature, and it does not rely on a known-good state. It targets the fundamental weakness of hiding rootkits, and turns the hiding behavior into its own detection mechanism

http://www.rootkit.com/newsread.php?newsid=338 this site has deeplevel analysis tools
http://www.invisiblethings.org/tools.html discover rootkits the rootkits are back for windows http://www.f-secure.com/weblog/archives/KimmoKasslin_VB2005_proceedings.pdf