Deus Ex: How to do a non-lethal takedown of an MJ12 Commando or MIB --- without the riot prod?
Solution 1:
MJ12
MJ12 are semi-ordinary human beings. I can confirm Albort's comment about the baton: in my non-lethal play-throughs I've taken out MJ12 with the baton and the strength mod. Possibly without the strength mod too -- I don't remember for sure.
You might want to try crouching and hitting them in the knees from behind: I know for sure that's more effective than a back-hit for the riot prod, and it might also be more effective with the baton. I believe head hits are more effective too. You probably know this, but the key is to catch them by surprise. As soon as they're alert, a nonlethal attack does way less damage.
You can also take them out easily with tranquilizer darts.
MIB
MIB are another story. The only non-lethal way I ever found to deal with them was to avoid them, or to take them out with tranquilizer darts. And boy, it takes a lot of darts. Also, it's been a few years, but it's possible they explode after falling unconscious... not sure about that.
As for a one-shot non-lethal MIB takedown: while I haven't obsessively tried every method (and this from someone who had obsessively played through the game eight times :-), I don't believe it's possible. They're incredibly tough.
Solution 2:
A non-lethal takedown is apparently possible with the baton (as well as the riot prod (which you've run out of...)). Using the baton seems to depend on how much strength you have invested in.
You might find some clues etc in this forum: http://forums.anandtech.com/archive/index.php/t-1228473.html
or this one: http://forums.eidosgames.com/showthread.php?t=35762
The general consensus seems to be that one-hit non-lethal takedowns require the strength biomod. If you havent invested in it, you could be fairly stuck...
Good luck though
Solution 3:
Non-lethal take downs with the baton on these guys require Low-tech skill to be upgraded, and use of the combat strength aug. Being stealthy is useful as well (there's a bonus there). For the tranq darts, upgrade of the Pistol skill is useful, as well as getting a head-shot (stealth useful here too).