The last readable newspaper, book and PDA in Deus Ex

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.

If you kill Lebedev

• You don't get any XP Points (!)
• Ana is pleased with your performance
• If you talk to Gunther at the helipad, you inform him that you killed Lebedev. Gunther congratulates you
• You receive a message from Alex that Manderley is pleased with your performance.
• You get 1000 credits op bonus. Manderley is happy that you followed his orders
• You will have to face Ana Navarre later on either in the subway in Battery Park after escaping Hell's Kitchen or in the Unatco HQ after you escape MJ12 prison

If you kill Navarre

• You receive 200xp points
• You get to hear the entire dialogue between JC and Lebedev (like sb mentioned, he dies after from the hands of MJ12 and you are getting blamed for it)
• Alex is freaked out by what happened but promises to erase the logs to cover for you
• If you talk to Gunther at the helipad, JC lies to him and tells him that there was a shootout at the 747. Gunther says he needs to investigate to check if Navarre is fine
• JC lies to Manderley about the 747 situation also, saying that Lebedev shot Navarre
• Gunther will discover you killed Navarre upon your escape from Unatco HQ
• You receive 1000 credits

If you don't kill neither Lebedev or Navarre - Ana kills Lebedev

• You receive 175xp points
• You get to hear most of the dialogue between JC and Lebedev
• Ana Kills Lebedev and expresses her disappointment in your performance
• If you talk to Gunther Hermann at the helipad, JC tolds him that Navarre executed Lebedev. Gunther says he will congratulate her
• Alex sends you a message upon reaching Unatco HQ, He says you shouldn't sweat it for not killing Lebedev
• Manderley is extremely pissed you didn't follow orders
• You receive 1000 credits anyways, after a short argument between JC and Manderley

Other soldiers at Unatco and general Carter will provide their comments based on your decision. Gen Carter will support your decision about not killing Lebedev (even if Ana kills him), he will be compassionate if you actually killed him, saying it must have been difficult.

In the end, Killing Navarre is the most advantageous choice - you get the most Xp and get rid of her early on. However, it is an extreme scenario in which you also loose some interaction with Navarre later on when you need to face her again and fight.

Not killing Lebedev seems the most logical, reasonable choice as it shows JC hesitant to finding his brother working for the terrorists and refusing to kill an unarmed prisoner.

Killing Lebedev is the least advantageous option as the player doens't receive any xp points. I find that very disappointing because it shows the game developers are "interfering" with your choices and punishing a player that chose to follow a difficult but direct order from his superiors. As much as I love Deus Ex, I found this quite dissatisfying that you're being "forced" to choose save or not kill Lebedev simply because those choices are more favorable.