AVG has one of the best free anti-virus programs around. They now have an anti-Rootkit tool:

AVG Anti-Rootkit is a powerful tool with state-of-the-art technology for detection and removal of rootkits. Rootkits are used to hide the presence of a malicious object like trojans or keyloggers on your computer. If a threat uses rootkit technology to hide itself it is very hard to find the malware on your PC. AVG Anti-Rootkit gives you the power to find and delete the rootkit and to uncover the threat the rootkit is hiding.