I can't speak for Windows, but the setup where I work involves four drives (currently 2 TB each), with three running as a triple-mirror ZFS pool. For backup, I split a drive off the pool, pull it, slide in the previous backup, and resilver the newly-inserted drive. Each time, I use a different drive bay.
The ZFS pool itself provides backup for several other systems, and snapshots are made periodically by a cron job to provide a further line of defense.
Here's what I use, though with different drives: Ubuntu + ZFS + rsnapshot. Works well, mostly declaratively configured, and ZFS means I don't have to worry about bit rot. It has its gotchas, for sure, but if you want your data to stay intact, this is the thing to use.
