If I have a bunch of boards, I depopulate them in steps. I start by plucking off individual components by hand with a pair of needlenose pliers with a twisting motion (Tantalum caps, crystal oscillators, Etc) and keep them sorted as I go. Then I use a big cardboard box with holes cut in it like a sandblasting cabinet and an air chisel to remove the junk components (electrolytic caps, low grade plastic connectors, metal etc) Then I do all of one type of component off all of the boards and keep them separated. (A wooden board with some nails pounded in it will give you something to brace the board against)
If you are careful with the angle you hold the chisel and use short bursts you can be very selective with the peices you remove and then just dump out the box as you finish each type of component. It does mean handling each board many times but that is much easier than trying to sort or separate them from a big pile and you'll thank yourself when you go to process them.