The muscular system is the bodily system that is composed of the muscles and serves the purpose of the movement of the body.
A diaphragm, a muscular membrane that separated the abdominal and thoracic cavities, was part of a diagram of the Human torso, stored in the USS Enterprise's library computer database. This database was accessed by the Talosians in 2254. (TOS: "The Cage")
Medical doctors often opt for inter-muscular injections instead of intravenous in Andorians because of their unique physiology. (TOS: "Whom Gods Destroy")
The prepared flesh and muscle of an animal, that is often used as food, is called meat. (TAS: "The Slaver Weapon", etc.)
Referenced parts of the system
Medical conditions affecting muscles
The final draft script of ENT: "Vox Sola" refers to myalgia, though this symptom isn't directly referenced in canon.