In Fallout 3, always the head. Sure, you can cripple the body, but an alternate and often quicker way of making them drop their weapon is making them dead. When I shoot freehand, it's the torso, in V.A.T.S., it's the head. Ironsights depends on the gun and the distance.
Fallout 2 though, once you have the proper weapon and stats, it's all about the eyes. Pair this with your lethal joke weapon (I'll spare you from TVTropes... this time), the Red Ryder LE BB Gun, and you're ripping apart Enclave soldiers with BBs.