mklink /J "C:\Users\yourname\AppData\Roaming\Apple Computer\MobileSync\Backup" "f:\yournewfolder\Backup"
You should see something like this in Windows 7. Note the little "shortcut" overlay icon? That's saying this is a link.
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You can also confirm it with dir from the command line. Note the <junction>:
C:\Users\Scott\AppData\Roaming\Apple Computer\MobileSync>dir
Directory of C:\Users\Scott\AppData\Roaming\Apple Computer\MobileSync
11/25/2011 10:10 PM <DIR> .
11/25/2011 10:10 PM <DIR> ..
11/25/2011 10:10 PM <JUNCTION> Backup [f:\iTunesMobileSync\Backup]
0 File(s) 0 bytes
3 Dir(s) 97,594,851,328 bytes free
If you are still on XP and not Vista or Windows 7, you don't have mklink, but you can use the junction utility in the same way for XP.
Havent tried with XP, it works with Windows 7, and its same utility for xp so definately it should work.