Thugs - You'll encounter these early on, they're dressed in black and armed with 10mm pistols. No problem. Two shots to the head is the max they can take. They'll generally have slightly less than 50 or 60 chest armor.
10.DD. Thug. Ninja wannabe, masked or unmasked. The unmasked one looks similar to the grunt, but wears a completely black uniform.
Commandos - Early on again, they're dressed in black like ninjas and carry submachine guns. Two or three headshots with the pistol will take them out of commision. They have a bit more chest armor than thugs, and about 40 leg armor. They'll jump kick you if you come in close.
Shotgun Commandos - Same as normal commandos but with shotguns. They'll often also have a small amount of head armor.
You won't be seeing Thugs or Commandos after mission 5.