We've just published a new beta version of our free BlackLight rootkit scanner, which now also supports Windows Vista (32-bit only) and Windows 2003 Server x64 Editions.
The same BlackLight executable will work on all supported platforms.
You may find it interesting that we're adding support for 64-bit operating systems, even though there are currently no rootkits for them! The reason is that while 32-bit rootkits do not work on 64-bit platforms it is not impossible to create a 64-bit compatible rootkit. It just requires extra effort.
For example, a user-mode rootkit would have to hook 64-bit processes with 64-bit code but also make sure everything is hidden from 32-bit applications running under WOW64 emulation. As the number of computers running 64-bit Windows has remained low, the rootkit authors have not had a reason to spend the extra effort to target those systems. When they do, we hope to be ready.