Supreme Commander is a military rank among the Asgard. Thor is titled Supreme Commander of the Asgard Fleet, acknowledging his position as the Asgard's commander-in-chief. (SG1: "Thor's Hammer", "Thor's Chariot")
The Goa'uld System Lord Ba'al later styled himself Supreme Commander of the Goa'uld Empire, essentially taking over the functions that Ra held as Supreme System Lord (SG1: "Reckoning, Part 1")