The captives are nothing more than normal wastelanders unfortunate enough to be captured by super mutants. However, most people in the wasteland say that they do not know why super mutants choose not to kill and eat their captives, but some events suggest two main reasons.
During the quest Big Trouble in Big Town, some humans from Big Town are captured by super mutants and held in the Germantown Police HQ. Apparently, these humans have been captured to be used as food. While in the building, a super mutant can be overheard conversing with a human who is about to be killed. The human asks why he is to be killed when there are plenty of human remains available (presumably from other captives). The super mutant jailor reveals that they prefer their food to be from a fresh kill.
Uncle Leo, a friendly super mutant, suggests that the captives are used to create more super mutants. This is corroborated by dialog overheard from other super mutants in other parts of the wasteland, who remark that they need more new recruits, and so they must abduct more humans to transform into super mutants (using "green stuff"), which would be consistent with the method of super mutant creation practiced by the Master.
Releasing captives results in a Karma boost. Care should be taken when trying to free them, as they will usually be in the same area as their captors. If you free a captive, they will thank you and offer some food, Rad-X, or ammunition. If you accept these supplies, you will receive 50 Karma points and the supplies. If you tell them to keep it, you will receive 75 Karma. There is no Karma penalty for leaving the captive to their fate. Most captives are killed right away after being freed as they run toward other enemies more powerful than them.
You will not lose Karma if you execute a captive.
If you ignore a captive or choose to leave them to their fate, a new captive will eventually respawn along with new super mutant guards if you revisit the location. However, if you free the captive, or if the captive is killed, no new captives will appear in that location.
The first captive you are likely to encounter is north of the Anchorage Memorial, where the fifth Keller tape is also located. The captive is in the tent behind the trucks, guarded by a level-appropriate super mutant and two centaurs. Be wary of the trucks, as it will kill the captive if you shoot them. Assuming you have followed the Wasteland Survival Guide quest early on, this should also be your first encounter with a super mutant. If you decide to escort the captive after freeing him/her, he/she will run to the northwest of the map near Fort Constantine, and will keep running beyond the northern map limit, stopping at a rock formation there for the remainder of the game.
One is halfway between the Jefferson Memorial and Rivet City, on a boardwalk at super mutant bonfire. It is difficult to walk between the two places without noticing a pocket of three to six super mutants. The mutant at the top holding a minigun stands next to the captive. There is also a Lying, Congressional Style book laying beside some ammunition cases and gore bags. Once freed, this captive runs up the Jefferson Memorial catwalk past the irradiated metro across the bridge, then past the Citadel, follows the road past Alexandria Arms, and stops next to a bus opposite the raider camp next to the flooded metro. He/she will run back to that spot if you try to move him/her. After a while, he/she will disappear. - Note: You may find this area completely deserted of enemies, so you can just walk in and free the captive (confirmed for all platforms).
Note that Crazy Wolfgang, Crow, Lucky Harith, and Hoff regularly pass through here (as it is part of their caravan route) and will be attacked by the super mutants. If you stumble upon them passing by, assist them in killing the mutants or they might get killed.
A captive located at the eastern highway entering the city. It is easiest to walk from Friendship Heights to Farragut West Metro station, enclosed in the city walls. The captive is guarded by a super mutant and centaur. If you continue west, you will find a small blockade with two mutants and a centaur, and a few gore bags. A mini nuke and two first aid and ammunition boxes are in this blockade.
There are two captives at Clifftop Shacks which is almost due north of the Minefield and west of Vault 92. The super mutants will approach you upon contact, giving you a chance to dispose of them without hurting the captives. However, this area is also the site of a 'Type B' random encounter, which may lead to a battle between the spawned encounter and the super mutants.
There are two captives in the Roosevelt Academy escape tunnels and maintenance section. If you release the captives before you completely clear the area of super mutants and centaurs, they will likely be killed in their escape, but you will not suffer any Karma penalty if that happens.
There is a random encounter in which two super mutants are holding a captive that can be rescued. The encounter may spawn at 'Type A' encounter sites near either Vault 87 or the German Town Police Station.
If you choose to follow and protect a captive, they will eventually stop and do nothing, offering no other interactions with the player. Their actual destination is merely a pre-programmed arbitrary location on the world map, sometimes beyond the normal map borders, and there is no benefit or reason to actually escort them besides curiosity.