This is not spyware, but a program to help you discover spyware! Track any and all changes to the registry and file system, and also record all shell notification events (e.g. media inserted), when a program is installed, uninstalled, or run. This can warn you of programs trying to install new services, programs that are set to run on reboot, changes to your home page, etc. It's a highly configurable program that allows you to catch any change to your system. Filtering lets you zoom down to the details that are most important to you.

Limitations:
Project has been abandoned.