You can choose which drives DBAN nukes or doesn't nuke, just don't tell it to "autonuke." Instead, hit ENTER to start it in interactive mode, then use the arrow keys and spacebar to select/deselect drives and hit F10 to start it. Or just unplug the drives you want to make sure you don't nuke by mistake.
If you have Win2000 Pro or WinXP Pro (not Home) then another option is to delete the partition on the drive you want to nuke, then create a new partition, and let's say you give it drive letter X:. You would go Start > Run > cmd to open a command window, then type cipher /w:X:\ and let it rip. That is correct as typed, there's no spaces between any of /w:X:\.
This fills all the unoccupied capacity with EFS-encrypted data three times, deleting it after each run. You could run cipher on your C:\ drive while you're using the system, nothing bad happens... it only does its thing on the unoccupied capacity of the drive.