A computer program was a set of instructions written by a programmer to run a computer or a specific creation such as a holographic program.
One of the assumptions for Arthur Malencon's death, killed by the laser drill, was a malfunctioning computer system. Later, it was revealed that a lifeform of the planet was responsible for the death. (TNG: "Home Soil")
An Iconian probe encountered by the USS Enterprise-D in 2365 transmitted a computer program to the starship, which started rewriting the ship computer's software in its own image. (TNG: "Contagion")
The first draft script of DS9: "When It Rains..." referred to a data-sifter, though this type of computer program is not referenced in canon.