It stood for Save Our Ship, and was transmitted when a seagoing vessel was in dire need of help. On Earth in the 19th century, the nearest ship was legally obligated to render assistance. (TOS novel: The Fearful Summons)
The system continued to be used in some form into the 24th century.
In the 2260s, a missing survey ship's continuous SOS was picked up by Nyota Uhura aboard the USS Enterprise along with its call sign. Unfortunately the vessel had crashed on Taunus and the crew died before they could be rescued. (TOS comic: "The Aging World")
Spock was surprised when the Enterprise picked up an SOS from Fomalhaut V. The planet was uninhabited according to computer records, and Morse Code was rarely used in the 2260s. Uhura adjusted the viewscreen to the source of the transmission, which showed dinosaurs rampaging through a city. (TOS novella: The Truth Machine)
- It is quite possible SOS was being used as a generic term for a more contemporary distress call system used in the 24th century.
- TOS episode & Star Trek 1 novelization: Miri
- TOS - Star Trek 2 novelization: Space Seed
- VOY episode: "The 37's"
- TOS novel: The Fearful Summons
- TOS novella: The Truth Machine
- TOS comic: "The Aging World"
- TOS comic: "The Mindless Ones"
- TOS comic: "What Fools These Mortals Be.."
- DS9 novel: Devil in the Sky
- NF novel: Blind Man's Bluff