MJ Registry Watcher is a simple registry, file and directory hooker/poller, that safeguards the most important startup files, registry keys and values, and other more exotic registry locations commonly attacked by trojans. It has very low resource usage, and is set to poll every 30 seconds by default, although you can adjust this to anywhere between 0 and 9999. A configuration file stores all your settings for future use.
MJRW not only polls the system, but it also hooks it, so that most changes to keys, files and directories are reported instantaneously. Key deletions are still caught by the polling loop though, since they cannot be hooked. Exactly which keys and files are protected can be completely configured by the user, although the sets I supply with MJRW will cover most standard PCs.