If they're all on the D drive they're probably quite safe. If there are any on the C drive that
aren't on the D drive copy them over. I would also get them all onto CDR at some point (or better still buy a 4GB or 8GB flash disk and copy all your important stuff onto that) but they'll probably be OK on the D drive for now.
Not sure what's causing your startup problems, like I said. There's no system restore built into Win 2000, so that's not an option. Not sure what to suggest other than trying to get hold a Windows 2000 disk and repairing the installation - think I have one you can borrow.
Still, I expect someone will come along soon who actually knows what they're talking about, so...