The one free program that can partition various types of partitions for both Linux and Windows is the Gnome Partition Editor. You simply boot with this to create one or more primary partitions on a drive. What decides which OS on drive loads is the boot loader which reads the master boot record(mbr).
For dual booting different OSs it will depend on which combination you are planning to install. With 2000 and XP, both running on NTFS partitions, 2000 would be first in line. The newer OS always follows the older since the newer is generally an upgrade. For Linux you would a Grub or Lilo boot loader to choose whick of the distros to load by entering commands at the Grub or Lilo prompt directing the loader to the root partition of the one selected. In XP and Linux yuo can install a universal boot loader into the mbr to make the selection that way.