For my carded ones, I put them in the order they appear on the back of the package.
As for my loose ones, Joes are together, Cobras are together. I usually start with a leader at the center of the shelf, and work my way out. Example: Cobra Commander is at the center, with Storm Shadow on one side and maybe a Crimson Guard or Destro on the other. Next to Destro would be Baroness, and next to
SS would be Mindbender......
It's to the point though that in order to display the figures, I need to push more together.
__._.··..-.__..__.——.·..__.—._.