MJ12 commandos are generally considered to be the toughest enemies in Deus Ex, these robotic servants of Majestic 12 first show up in Hong Kong and become increasingly more common in the levels that follow. Their main weapons are turrets mounted to their arms that fire rapidly at you, they also have a secondary attack that fires missiles at you. So... how do you beat them?
One very obvious solution is not to engage these enemies to begin with. Sneaking past enemies is almost always possible for a skilled player and some augmentations grant you silent running for when you are in a haste. When spotted you can also retreat into cover and after a while the enemy will give up, commandos are also unlikely to come looking for you after initially spotting you (unlike some regular soldiers).
the easy way
Like most other enemies, a LAM grenade or rocket will instantly kill a commando. Having a GEP on you is very advisable for this. Keep in mind that explosions tend to attract at least some attention from enemies.
Despite of what you may think at first sight, a commando is most certainly not invincible. Using assault-rifles, shotguns and pistols will eventually take them down, but this is not advisable. Headshots with snipers and pistols are efficient though and can be used when other methods are not available.
This is by far the easiest way to deal with these bastards, but it may not occur to you naturally. A good shot from the stun-rod will take down a commando instantly and peacefully, but even more efficient is using the Dragon Tooth sword that you get in Hong Kong as part of the storyline. This sword will take down a commando in two hits and regular enemies in one (your skill in melee weapons is almost completely irrelevant). To make this work I advise luring enemies around a corner and striking them down before they spot you.
Using explosive or the Dragon Tooth render commandos almost completely harmless, but there is another enemy you should still watch for. The Men in Black (and their female versions) explode upon killing them and using melee weapons against them will likely drag you along with them into the afterlife. I advice sniping them or stunning them before they can do anything (they can wield any weapon, including plasma guns). Have fun and I hope this advice helped you past those nasty commandos!