RootkitRevealer is an advanced rootkit detection utility. It runs on Windows NT 4 and higher and its output lists Registry and file system API discrepancies that may indicate the presence of a user-mode or kernel-mode rootkit. RootkitRevealer successfully detects many persistent rootkits including AFX, Vanquish and HackerDefender (note: RootkitRevealer is not intended to detect rootkits like Fu that don't attempt to hide their files or registry keys). If you use it to identify the presence of a rootkit please let us know!
The reason that there is no longer a command-line version is that malware authors have started targetting RootkitRevealer's scan by using its executable name. We've therefore updated RootkitRevealer to execute its scan from a randomly named copy of itself that runs as a Windows service. This type of execution is not conducive to a command-line interface. Note that you can use command-line options to execute an automatic scan with results logged to a file, which is the equivalent of the command-line version's behavior.