I don't think this is the appropriate place to ask this question, but I'll give it an answer anyway.

Yes, Windows 3.1 and 9x run "on top of" DOS. Windows 2000, XP, and NT, however, do not. They still have DOS functionality (go to Start -> Run -> cmd or command). You can't boot straight into DOS on 2000, XP, or NT, but you can still use a 9x boot disk and what not.

I don't believe there is a built-in defrag program in DOS, or the DOS shell, but you could probably find something online and run it in DOS or in the shell.

Hope this helps,

D'elTarra