Quicklist for migrating partitions:

• Download Knoppix LiveCD
• Burn and boot to said CD
• umount any partitions that you will be moving
• Use gParted to "Copy and Paste" partitions to intended destinations (yes, even across harddisks). Don't forget to create the swap fs!
• Take notes where each partition is and what it contains. Map to expected /dev/sdxx devices so you know what's where
• Shutdown and move around / disconnect harddisks if needed
• mount filesystems for /boot and /etc (may be on one filesystem
• edit /boot/grub/device.map file to reflect changed harddisk organisation (or whatever other hoops other boot managers make you jump through)
• reinstall GRUB (or other boot manager). something like this
  • find /boot/grub/stage1
  • Use output for next command  root (hdx,x)
  • Setup grub with setup (hd?) where ? is whatever disk (for MBR install) or where ? is whatever partition (for partition install).
• Edit /etc/fstab to point to correct partitions, delete obselete lines from the file.
• Reboot and test. Also prepare to reinstall windows, if needed... :(