Commander was a rank used by the service organisations of many civilisations.
Known Commanders
Time Lord
Both the Chancellory Guard and Capitol Guard had Commanders among its ranks. They reported directly to the Castellan. (TV: The Deadly Assassin)
Hilred was a Commander of the Chancellory Guard when the Decayed Master attempted to frame the Fourth Doctor for the murder of the President. (TV: The Deadly Assassin)
Andred was a Commander of the Chancellory Guard during the Vardan invasion. (TV: The Invasion of Time)
Maxil was a Commander of the Chancellory Guard. (TV: Arc of Infinity)
During the Death Zone, a Commander of the Chancellory Guard carried out a search of the quarters of Jerricho on the orders of Lord President Borusa and discovered the Black Scrolls of Rassilon. He later shot Jerricho dead as he tried to escape. (TV: The Five Doctors)
Hallan was a Commander and had been a personal bodyguard to many Lord Presidents of Gallifrey. (AUDIO: Imperiatrix)
Raldeth was a Commander in the Chancellery Guard during the Dalek invasion of Gallifrey. (AUDIO: The Apocalypse Element)
Veklin was a Commander during the Last Great Time War. (AUDIO: The Lady of Obsidian)
Roxita was a Commander of the Capitol Guard during the Last Great Time War and led a guard detail out with Cardinal Ollistra to Synthesis Station. (AUDIO: Day of the Vashta Nerada)
Partheus was Commander of a Battle TARDIS which led the mission to the Tantalus Eye. (PROSE: Engines of War)
Kenossium was the Time Lords' military commander during the Last Great Time War. (TV: Hell Bent)
Human
A Commander was the leader of an exploration mission from the Earth Empire. (TV: The Sensorites)
Another Commander was the head of the Collector's Inner Retinue on Pluto. (TV: The Sun Makers)
The Knight Commander was the leader of Morgaine's men. (TV: Battlefield)
Henry van Statten's private army was led by a Commander. (TV: Dalek)
Hachiman was a human commander in the Human-Galatean War. (COMIC: The Child of Time)
One Commander was an Auton posing as a Roman commander, whose appearance was based directly on Amy Pond's memories of a book she owned on Romans. (TV: The Pandorica Opens)
Sontaran
The Sontaran Empire had various Commanders of its Divisions, Fleets and Squads.
Stor was a Commander in the Sontaran Special Space Service and the leader of the forward task force in the attempted Sontaran invasion of Gallifrey. (TV: The Invasion of Time)
Steg was the leader of Sontarans invading the Tiger Moth. (HOMEVID: Shakedown: Return of the Sontarans, PROSE: Shakedown)
Skorr and Kaagh served under General Staal during the Tenth Sontaran Battle Fleet's invasion of Earth in 2009. (TV: The Sontaran Stratagem, The Last Sontaran)
Stark was a Commander and planned with the Alliance to trap the Eleventh Doctor in the Pandorica in 102, believing him the one causing cracks in the universe. (TV: The Pandorica Opens)
Strax was a Commander who was forced to serve as a nurse to restore the honour of his clone batch. (TV: A Good Man Goes to War)
Halke was a Commander who was trapped by the Minotaur on its prison ship and was killed by it. (TV: The God Complex)
Linx was a Commander in the Fifth Sontaran Army Space Fleet. (TV: The Time Warrior)
Skarr was a Commander who infiltrated the town of Christmas during the Siege of Trenzalore. (TV: The Time of the Doctor)
Dalek
The Dalek saucer commander was the designated commander of the Dalek flying saucer during the 22nd century Dalek invasion of Earth. (TV: The Dalek Invasion of Earth)
The Vega VI Dalek commander was commander of the invasion of the planet Vega 6. (AUDIO: Invasion of the Daleks)
One Dalek Commander was in charge of the Dalek operation on the planet Ecros to test the Dalek driller. (COMIC: The Dalek Revenge)