I have a win98 laptop that I'm going to have to use for my upcoming finance class. Because of this, I'm learning how to clean up a win98 install (msconfig.exe to kill unwanted startup programs, cleaning up drivers so windows shuts down nicely, etc.). The cool thing about Cygwin is that you can see (via ps -aW) Windows system threads. The bad thing is that you can't kill them. ;).
Oh yeah, and keeping backups of drivers you've installed is also a good idea. For some reason, drivers will occasionally corrupt in win98. I have no idea why. Maybe I'll get a book on win32 internals, and maybe I'll bring it to the tentative Saturday BBQ, where I'm known as a linux geek. That'll cause much chagrin.