Remember Mark Russinovich's analysis of the Sony Rootkit? Have you used any of the Sysinternals tools such as Filemon, Regmon and Process Explorer?
In addition to the tools mentioned above, there is also RootKit Revealer, Autoruns (to see what is configured to start at login when your system boots) , and more. Sysinternals' tools have been widely used by the security community when evaluating what may be on a person's computer.
Mark Russinovich's statement at "Mark's Sysinternals Blog" in "On My Way to Microsoft!" that
. . . Microsoft is still evaluating the best way to leverage the many different technologies that have been developed by Winternals. Some will find their ways into existing Microsoft products or Windows itself and others will continue on as Microsoft-branded products. . .is somewhat reassuring. Losing those utilities developed by Mark and Bryce Cogswell would certainly have an impact on both the security community and the public. On the other hand, incorporating some of those features into Microsoft products (under Mark and Bryce's guidance, of course ), can have a very positive effect on Microsoft software.
As hearty as my congratulations are to both Mark and Bryce, I certainly hope that this change in landscape won't end up with the loss of an independent voice as well as the "can do" attitude provided throughout the years.
Microsoft Press Release
Winternals Press Release