(written from a Production point of view)
Myalgia is, simply put, muscular pain. In the final draft script of ENT: "Vox Sola", Denobulan Doctor Phlox notified the survivors of a symbiotic lifeform, which had infested Cargo Bay Two of Enterprise NX-01, that they would likely experience mild myalgia for about a day. Those expected to feel muscular pain included Captain Jonathan Archer, Commander Charles Tucker III as well as Crewmen J. Kelly and Michael Rostov. The myalgia was caused by them having been entangled and hung up in the organism's web. In canon Star Trek, myalgia has never been referenced.