Use an external hard drive
A virus wont affect your second drive if all your using it for is backup.
I would have thought a virus could only access the drive if you opened the said drive,
then again I could be wrong.
Hmm,fair enough I may have to rethink my backup strategy,A virus can do whatever it wants, its fairly trivial to just loop through all drives in explorer scanning them for executables to infect.
Its fairly clunky but the only way I can think of to do this is to truecrypt (http://www.truecrypt.org/) the entire drive and then only unlock it when you want to backup to it and then re-lock it afterwards. However don't lose your password as otherwise your paddle-less up the creek
and export the backup file to the ubuntu hdd then this seems pretty safe to me?backup software which creates an archive file of its own format (such as Acronis or similar).