Damn vista... I had it for a week and when I tried win7, vista got immediately kicked from my pc. I suppose you want to save your data temporarely to format the hdd or something similar... For windows systems and optical drives there are basically two file systems: CDFS (iso9660 and extensions) and UDF, which are supported in the usual linux distros. (and possibly apple's HFS, I don't know for shure this one).
If you have more than one partition (excluding vista's one with the windows folder) you can always save the data to the other one. If you reinstall vista (without formatting partitions) it only clears the windows folder and others like users data, programs (can't be shure about this one) and their data.
and there are the portable usb drives...
Oh, and you can always come back to our beloved and very old
windows xp. If upon installing it can't detect your hard disk, use nlite and integrate your motherboard drivers (you only need the southbridge ones).