Windows is basically DOS, so by running Windows, you have DOS which can be handful for those old picky DOS programs you can't live without, or for FlashROM updates that won't run in most other OS. However, you cannot boot into a DOS command line with Windows ME, so the last advantage of using Windows is now GONE!
Windows's "Dangerous Memory Model" allows any Win32 apps to write to critical memory area that should be protected, like the VxDs area where, for example, the disk cache is located. Imagine if by mistake one wrote to the disk cache and wrote bad data to your HD. The unreliable FAT would probably not recover from that and the system would not reboot and all data would be lost. oulala...
DOS/Windows is a technological dead end. x86 computing will eventually come to an end in about 5 years due to its technological limitations. By then, DOS/Windows cannot exist anymore as porting DOS/Windows to another platform than x86 would be a bankrupting task which Microsoft is not willing to do, or could even do. Moreover, Windows does not and will not run on SMP machines which means its life span may be even less than 5 years.
Its ancient FAT12,16 and 32 file system is very unreliable and fragments very easily. It also needs to use a hidden directory kludge which uses a lot of space just to store long filenames on these partitions.
Windows has been proven to contain a lot of security holes. Microsoft just keeps patching them up, but a lot of them are still left. Your data could be stolen by someone who found a new security hole pretty easily if they had interest.
DOS/Windows is the operating system for which the vast majority of viruses exist and are still being made. No other operating system have virus problems, not counting Microsoft Office macro viruses.
Windows is a single-user operating system with no access security what so ever on the workstation side other than a screen saver password. Expensive packages need to be bought to protect Windows from intruders.
Windows drive letter assignment is at the mercy of partition orders which can lead to an unbootable system or broken applications if partitions are changed. Moreover, Windows can only boot from "drive C:" because of DOS.
And don't even think about using Windows as a server.