A rootkit is a program (or combination of several programs) designed to take fundamental control (in Unix terms “root” access, in Windows “Administrator” access) of a computer system, without authorization by the system’s owners and legitimate managers. Access to the hardware (i.e., the reset switch) is rarely required as a rootkit is intended to seize control of the operating system running on the hardware. Typically, rootkits act to obscure their presence on the system through subversion or evasion of standard operating system security mechanisms. Often, they are Trojans as well, thus fooling users into believing they are safe to run on their systems. Techniques used to accomplish this can include concealing running processes from monitoring programs, or hiding files or system data from the operating system. — wikipedia
Using Sophos Anti-Rootkit is easy. Whether you use its simple graphical user interface or run it from the command line, you can easily detect and remove any rootkits on your computer.
McAfee Rootkit Detective
McAfee Rootkit Detective is a program designed and developed by McAfee Avert Labs to proactively detect and clean rootkits that are running on the system.
McAfee Threat Center
Trend Micro RootkitBuster
Trend Micro RootkitBuster is a rootkit scanner that scans hidden files, registry entries, processes, drivers, and Master Boot Record (MBR) rootkits. In addition, RootkitBuster can also clean hidden files and registry entries.
Panda Anti-Rootkit shows hidden system resources, identifying known and unknown rootkits. It analizes hidden drivers, processes, modules, files, registry entries, SDT modifications, EAT hooks, modification to the IDT, non standard INT2E and SYSENTER, IRP hooks. Unlike other anti-rootkit utilities which merely “reveal” hidden objects, Panda Anti-Rootkit positively identifies known and unknown rootkits and gives the option of removing them, including their associated registry entries, processes and files.
 List of Free Anti-Rootkit/Rootkit detection software for Windows ( ) [www.windowsreference.com]