You could boot up with floppy linux from
http://www.toms.net/rb/ . With that you can clean out the boot sector with a command like:
dd if=/dev/zero of=/dev/hda bs=512 count=1
Also, you can run linux fdisk from there to create or remove partitions.
Sometimes I use a WindowsMe boot floppy with the extras removed. I added a neat partitioning tool from
http://www.ranish.com/part/ . This is a very handy tool to have around and it's even encluded on another Very useful tool called
system rescue cd and you can get that here.
http://www.sysresccd.org/ .