Commander

Commander was a rank used by the service organisations of many civilisations.

Time Lord
Both the Chancellery 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 Chancellery Guard when attempted to frame the Fourth Doctor for the murder of the President. (TV: The Deadly Assassin)

Andred was a Commander of the Chancellery Guard during the Vardan invasion. (TV: The Invasion of Time) He later became castellan. (AUDIO: Insurgency)

Maxil was a Commander of the Chancellery Guard. (TV: Arc of Infinity) He was promoted to castellan following Andred's supposed death, (AUDIO: Lies) but later demoted to commander once more after siding with Pandora and Darkel in the civil war. (AUDIO: Appropriation)

When several incarnations of the Doctor were sent to the Death Zone, a Commander of the Chancellery 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)

Vrail was a commander with the Interior Defence Unit. (AUDIO: Assassins)

The General 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)

Bill Janson was the commander of Project S.W.O.R.D.. This was the subject of a question asked by Agent Twenty One in a quiz. (PROSE: )

In a parallel universe, William Riker was a Commander of the Federation Starfleet and first officer of the USS Enterprise (NCC-1701-D). (COMIC: Assimilation²)

Sontaran
The Sontaran Empire had various Commanders of its Divisions, Fleets and Squads;

A Sontaran commander was leader for the ones who fought the First Doctor, the first of the Time Lord's incarnations to encounter their kind. (AUDIO: The Sontarans)

Linx was a commander in the Fifth Sontaran Army Space Fleet. (TV: The Time Warrior)

Stor was a commander in the Sontaran Special Space Service and the leader of the forward task force in the  Sontaran invasion of Gallifrey. (TV: The Invasion of Time) Strumm was also a commander in the same unit. (AUDIO: Peepshow)

Loxx was a commander and also the second-in-command to Major Karne. (PROSE: Lords of the Storm)

Lork and Strek held the rank of commander. (AUDIO: The First Sontarans)

Steg was the leader of Sontarans invading the Tiger Moth. (HOMEVID: Shakedown: Return of the Sontarans, PROSE: Shakedown)

Lerox, a pacifistic Sontaran who helped Rose Tyler and the Tenth Doctor to stop the treachery of Colonel Snathe, held the rank of commander. (COMIC: The Betrothal of Sontar)

Jask was a commander of the Ninth Sontaran Battle Fleet who met the Eighth Doctor during the Last Great Time War. (AUDIO: The Sontaran Ordeal) A Sontaran with a similar name tried to kill Mickey Smith and Martha Jones, only to be knocked out by the Tenth Doctor with a hammer blow on the probic vent. (TV: The End of Time)

Skorr and Kaagh were commanders who served under General Staal of 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)

Merx was a commander under Marshal Skar of the Sontaran Empire's Eighth Battle Fleet. (AUDIO: The Sontaran Project)

Kygon Brox was a commander of the Eighth Sontaran Battle Fleet when he met the Twelfth Doctor, Clara Oswald, Field Marshal Rommel, and some Tuareg on the Sahara Desert on 1941. (COMIC: The Instruments of War)

Halke was a commander who was trapped by the Minotaur on its prison ship and was killed by it. (TV: The God Complex)

Skarr was a commander who infiltrated the town of Christmas during the Siege of Trenzalore. (TV: The Time of the Doctor)

Skaak was a commander who led the Sontarans in the Crimean war in Sevastopol in an alternate 1855, as part of Commander Ritskaw's plan to invade Earth's history with time-ships (TV: War of the Sontarans)

Stenck was the commander of the Sontaran invasion of Earth in late 2021, who planned to exploit the Flux event (TV: The Vanquishers)

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 Ercos to test the Dalek driller. (COMIC: The Dalek Revenge)

Before being named as leader of the Cult of Skaro by the Dalek Emperor, Dalek Sec was the Dalek Commander of the Seventh Incursion Squad. (PROSE: Birth of a Legend)

Other
Restac became a Silurian Commander after killing Malohkeh.

Oberon was a commander who helped the Seventh Doctor and Ace to defeat the Kla-Shi-Kel.

Behind the scenes

 * A generic UNIT commander features as a character in the video game Doctor Who: Legacy.