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Some antispyware tools (for example HijackThis) can provide a snapshot of important parts of the registry and as such are useful in a wider context. Unfortunately Hijackthis cannot be used in batch mode (or at least I do not know how to use it in a batch mode).
As for monitoring generally periodic snapshots are enough (it's a good practice to dump the content of important parts of your registry in the morning or at the end of the day; it can be a scheduled job), but there are specialized tools too.
Several tools from Microft Resource Kits for Windows can do snapshots of the registry:
Windows 2000 Resource Kit Tools
| RegSafe
Professional Edition 2.0 is a suite of tools designed to provide
Network Administrators, IS/IT professionals and Power Users with the
ability to perform advanced Registry management on 32-bit Windows
PCs. RegSafe provides comprehensive Registry editing and
management capabilities not found in other professional level
Registry editing tools, all from within a protected environment.
Top 5 Reasons For Using RegSafe®
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Last modified: March 15, 2008