You can use scheduled tasks to do this.
You’ll find scheduled tasks in Accessories on the start menu (in XP)
Schedule your torrent software (or whatever) to start at 3am daily.
Schedule a shutdown task for 6am (shutdown.exe is located in Windows\System32)
If your download software doesn’t restart when your system boots, you can add the /r param to the shutdown task’s command line and it will simply reboot rather than shut down. (If you need the system on for some reason)