Akira making it through the massive vents and tunnels of the underground city beneath Tokyo Landfill #1 to escape the assassins hunting him makes sense (and he finds himself reminding his prepubescent rescuers that he is not as compact as they are).
In an inversion from volume 7, after a Manchurian Agent locks down Mina's skyscraper-cum-palace the only person who can get to the security center via the way-too-small-for-anything-remotely-human vents is Vera (who turns into mist and is obliged to leave her clothes behind).
In Dragon Quest: The Adventure of Dai, Maam, after breaking out of her jail cell, evades the undead monsters in the underground dungeon through one such passageway. She's able to squeeze her way through it, though she remarks that either the hallway is getting narrower and narrower or she might need to go on a diet.
Justified in Excel Saga in Kabapu's underground base; as Dr. Shiouji pointed out, they have to be big in order for any sort of air to move though such a large place underground.
While searching an enemy ship in Fairy Tail the Exceeds (who are about the size of a cat) are shown crawling through an air vent, wondering about the necessity of it and complaining about how narrow it is. When they ask why they're in there instead of searching the rooms like a normal person, Happy says "No particular reason".
Franken Fran has to cut off at least half her body in order to pull off a vent escape.
Justified in Fullmetal Alchemist: shrimpy Edward is the only character who can fit in the air vents, and for him it's a tight fit. Which leads to further comedy as Ed has a complex for being The Napoleon.
Like the opening of season 1, the opening of season 2 is all about showing off the awesome skills of Section 9 while providing a reason for the unit's reactivation. The regular SWAT unit attempts an assault on the Chinese embassy through the air vents, but spectacularly fails with one officer dead and another being added to the terrorists' hostages. Seeing these poor results, his superiors immediately give Aramaki the green light to send in his team and get the job done.
When Batou is snooping around in Zaitsev's office, he hides in the ducts when Zaitsev returns unexpectedly.
2nd GIG episode "Ambivalence". Major Kusanagi physically breaks into the Cabinet Intelligence Agency's building to cyberhack into its Decatonchire server. After the Big Bad Goda discovers the breach and alerts security, she escapes the building by entering the air system via a opening in the ceiling.
Seras and Walter also use this to avoid a confrontation with the Valentine brothers.
Walter actually makes a point of reminding Integra that she used the vents to hide, so it's possible that they were deliberately designed with the purpose of allowing people to move throughout the mansion and avoid enemies in mind.
In Hetalia: Axis Powers, Paint it White!: Italy, Germany, and Japan pull one of these in order to escape the aliens currently chasing them. May or may not be justified because they were in an alien mothership, with air vents about the size of an average person. They DID fall through at one point, and Germany got quite a few scratches to the face.
Done in Hunter × Hunter, though the character doing this (Queen Oito, after Kurapika grants her Nen abilities) is mind-controlling a cockroach, making it more plausible than normal. The cockroach finds Prince Tserriednich's Nen Beast within the ducts, forcing Oito to perform a quick mind-recall back to herself before the Nen Beast eats the cockroach.
In Mission: Yozakura Family, the Yozakuras often find themselves entering and leaving facilities by crawling through the air ducts in classic spy fashion. But the story points out how cramped these things usually are, and the Yozakuras are trained to dislocate and relocate their own bones at will in order to fit. Unfortunately for Taiyo, he's not nearly as well-trained and recoils in pain when he performs a Dramatic Dislocation.
Subverted with glee in Mnemosyne: Slender (though busty) Action Girl Rin Asougi decides to infiltrate an empty research laboratory by going through the ducts. She predicts the lasers and makes them visible by filling the cramped ventilation duct with smoke from a cigarette, and then proceeds to slip under the lasers... until her butt catches the laser, setting off all the alarms. Cue Rin's capture and... Squick.
In Monster, Johan and Anna/Nina's mother escapes through a rather small-looking air vent not just pregnant but in labor.
Neon Genesis Evangelion: Asuka, Rei, and Shinji were forced to use this route to get into the Geo-Front during a power outage when none of the doors would open. The air vent entrance also lampshaded the Male Gaze when Asuka kept kicking Shinji for "looking ahead." Later in the episode, we are treated to the sight of Humongous Mecha escaping via (humongous) air ducts. The geofront itself is an immense underground open space, hence the need for extremely large duct shafts to the surface to keep the air fresh.
In Shugo Chara!, Kiseki and Yoru escape from a locked room this way. Justified since the Shugo Charas in that series are small enough to fit in normal air ducts.
Successfully done by Tsukiyo in The World God Only Knows, but small as she is she still couldn't have pulled it off normally. Rather, she was shrunk down to the size of a doll and it was still a pretty tight fit.
Mokuba Kaiba once escaped from the Big 5 this way in Yu-Gi-Oh! At least he's a fairly small kid, more likely to fit and all that.
In Yu-Gi-Oh! R, Jounouchi and Honda avoid some Mooks this way. Lampshaded by Jou, who complains about how claustrophobic it is and keeps getting accidentally kicked in the face by Honda.
In Yu-Gi-Oh! ARC-V, a few characters escape from prison this way. It takes them a while to remove the grate and the fans inside, and a guard catches them, but they manage to bluff that they had been ordered to repair it.