There is a backup system built into OneNote. Tools | Options | Backup lets
you set the backup interval and number of backups to keep. The backup files
are stored in the location set under Tools | Options | Open and Save | Backup
Folder. You can set that to a folder on a network or other media, and
control restoration of older sections, by choosing File | Open Backup...
The files in your OneNote Notebook are created by default in "C:\Documents
and Settings\<yourname>\My Documents\My Notebook". Everything under the "My
Notebook" folder should be backed up if you're doing it manually.