In the *nix world, package managers have mostly done a good job of fixing this problem. In this spirit, Secunia has released their Personal Software Inspector, which will alert you when *security* patches (not every update, much like security.debian/ubuntu.org) are available for over 4200 apps. It does this by using file signatures and .dll/.ocx version numbers. Communication with the Secunia servers is secured with SSL, and they only collect version information and not personal info. At worst, they will know who is using which apps, but they claim to delete even that info after 12 months, so not a large privacy concern.
This could be a useful tool beyond the personal desktop by adding it to the auditor's arsenal. When auditing a machine, give the PSI a run, and see if *all* apps have been patched or just windows.