I've put together a couple of batch files that protect the registry, autostart folders and core system files from undesired changes or additions. They're written for Win98 but may ALSO work on WinME. Instead of trying to prevent changes in real time, the first makes backup copies of the files. The second is called during boot before windows STARTS and OVERWRITES the existing files with the backups.
If anything has added entries to an autostart location, it's automatically overwritten when the PC is rebooted.
Most likely, the batch files will have to be edited to match your particular system. The pages are written with the inexperienced user in mind. They may go into more detail than many here would need, but I'd RATHER err on the side of caution. Feel free to use and modify them for your needs.
http://www.freewebs.com/herbalists/index.htm
They do not work on NT, 2K, or XP If anyone uses them on WinME, let me know what you needed to modify and I'll ADD it to the page.
Rick

Soory about using a free site. It's all I have available.