Ventilation systems were used throughout buildings, starships, starbases and other facilities to direct and control the flow of breatheable atmosphere. (TOS: "The Trouble with Tribbles";VOY: "Year of Hell, Part II", "Message in a Bottle")
Turkana City had a ventilation and recirculation complex in one of its underground levels. (TNG: "Legacy")
Map of Turkana City showing various underground levels, including its ventilation and recirculation complex
In 2268, on stardate 3619.2, the Dikironium cloud creature entered the USS Enterprise's ventilation system and subsequently killed one crewman and severely injuring another. Captain James T. Kirk, Commander Spock and Doctor Leonard McCoy then met and decided to drive the creature out of the ventilation system the ship by flooding the system with radioactive waste. (TOS: "Obession")
Later that year, on stardate 4523.3, Tribbles infested Deep Space Station K-7 by moving through the station's ventilation ducts allowing them access to the station's grain storage area. (TOS: "The Trouble with Tribbles")
In 2269, on stardate 4978.5, the crew of the Enterprise became intoxicated by the affects of Harry Mudd's love potion which was desiminated throughout the ship through the ventilation system. (TAS: "Mudd's Passion")
In 2374, on stardate 51425.4 (Day 133 of the Year of Hell), the ventilation system onboard the USS Voyager) began to fail as a result of constant attacks from the Krenim Imperium which allowed gas from a class-9 nebula to flood one of the last habitable decks. (VOY: "Year of Hell, Part II")
Later that year, on stardate 51462, The Doctor and the EMH Mark II of the USS Prometheus dispersed Neurozine gas throughout the Prometheus using the ventilation system, incapcitating the Romulan hijackers. (VOY: "Message in a Bottle")