Most of these televised sources are heavily dubious, and need better citations.
A respiratory bypass system was a part of Gallifreyan physiology which allowed Time Lords to go without breathing for longer periods of time than most humans could. (AUDIO: Return of the Krotons) It also allowed them to filter out unpleasant smells. (PROSE: Cat's Cradle: Witch Mark)
The Doctor used it to survive more than once. The Second Doctor credited his survival on the surface of Mnemosyne to his respiratory bypass system. (PROSE: The Wheel of Ice) The Fourth Doctor used his respiratory bypass system to survive being strangled by an Osiran service robot. (TV: Pyramids of Mars) He later used it to avoid inhaling helium. (TV: The Robots of Death) The Fifth Doctor used it to survive brief exposure to the vacuum of space, (TV: Four to Doomsday) to recover from being hanged (PROSE: A Town Called Eternity) and to retrieve the milk from a queen bat in an airless cavern. (TV: The Caves of Androzani)
The Sixth Doctor avoided hypoxia when he shut down atmospheric controls to the mines on the planet Onyakis to defeat the Krotons there, (AUDIO: Return of the Krotons) using this advantage again to avoid breathing in vorum gas. (TV: The Two Doctors) In his seventh incarnation, the Doctor used his respiratory bypass system to avoid being overcome by ether. (PROSE: Timewyrm: Genesys)
When the Doctor's second heart was extracted by Sabbath in his eighth incarnation, one of the abilities the Doctor lost was the respiratory bypass system, leaving him vulnerable to being strangled until Sabbath allowed the heart to die and the Doctor to grow a new one. (PROSE: The Adventuress of Henrietta Street, Hope, Camera Obscura)
River Song had a respiratory bypass system, but she hadn't used it very much. When she and Isabella Clerkwell were trapped in a room where the air had been sucked out, Isabella passed out and River struggled to remain conscious. She tried to activate her respiratory bypass system but due to her lack of practice with it, she didn't have enough time to activate it. (AUDIO: I Went to a Marvellous Party)
Despite its usefulness in various occasions, the bypass system still has its limitations. The Twelfth Doctor suffered seemingly permanent blindness after he was forced to expose himself to the vacuum of space when traversing the exterior of a space station, as he was forced to donate his spacesuit's helmet to his companion Bill Potts when hers was damaged (TV: Oxygen)