The shoulder was the upper part of the torso which connected the torso with the arms and consisted of muscles, bones, and skin.
Clothing such as a cloak or suspenders were worn over the shoulder. (TOS: "Shore Leave"; TNG: "The Big Goodbye")
A metaphor said "someone is looking over your shoulder" what stood for a kind of spying. Jonathan Archer expressed his concerns about the Vulcans using this metaphor in 2151 in a conversation with T'Pol. (ENT: "Breaking the Ice")
Spock's "multi-legged creature"
Spock once told an Eminian guard that "[t]here's a multi-legged creature crawling on your shoulder," before reaching towards him and applying a neck pinch. (TOS: "A Taste of Armageddon")
In 2268, after Hikaru Sulu had been touched by Losira, Doctor Leonard McCoy discovered a layer of necrotic tissue a few cells thick in his shoulder. (TOS: "That Which Survives")
O'Brien suffering from a dislocated shoulder
In 2366, Miles O'Brien suffered from a dislocated shoulder following a kayaking accident on the holodeck. An osteotractor frame was used to cure him. (TNG: "Transfigurations") Eight years later, O'Brien suffered again from a dislocated shoulder. (DS9: "Inquisition")
Miles O'Brien also injured his shoulder in a darts game against Vulcan Starfleet officer Syvar. (DS9: "Shakaar")
In 2369, Doctor Julian Bashir performed a neuromuscular scan of Major Kira Nerys's injured shoulder. (DS9: "Battle Lines")
Var'Hama candles were ceremonial Klingon candles made from the tallow of boiled targ shoulders. (DS9: "You Are Cordially Invited")
In the game of hockey, a high stick was a violent move in which the hockey stick was raised above the shoulder. (VOY: "Critical Care")
In 2380, Lieutenant Shaxs compared his security team on the USS Cerritos to a bear pack, he said they walk "shoulder to shoulder." (LD: "Envoys")