The equivalent in the win world to obscure command line settings is the registry. There is a whole heap of documented and undocumented config in there. 99% of the time you don't really need to go in there, but its often the more automatable way and occasionally you will find some fun options.
Mm, I still recall the time my Windows 98 installation corrupted its registry somehow. The only fix was to reinstall, and the machine had no floppy or CD drive... getting Windows back on there was a task.
No floppy or CD? You were just asking for trouble then IMHO. It was common to have to reinstall windows every 6-9 months in the win9x days. That didn't even really work for ME, but by then win2000 came in to save the day. Software was primarily distributed on CD those days, being without a CD drive must have been a huge hardship.
I vividly remember having to reinstall Windows also in the XP days at least once a year due to malware or due to anti-malware software slowly strangling the OS.