Angels 2200: Loser uses one when they attempt to "rescue" Quetz
Subverted in Freefall, when Sam finds out the hard way that the air ducts on his ship are not quite big enough for him to hide in. He might have succeeded if he had ditched his encounter suit.
Justified in Schlock Mercenary, as Schlock is a carbosilicate amorph — he can squeeze through air vents no matter how small they are — well, except for his eyes (standard Sphere Eyes) and his plasgun (big).
Subverted: Casey sneaks in through the airvents, but is met by the Mime Assassin inside the air vents, as the villain had been expecting the plan.
The C&A villain Lord Milligan follows the Path of the Villain as a religion and deliberately follows every cliche. Including having giant air ducts.
They try the air vent route multiple times, and the mime-assassin is in there every single time. Including the last time, when they were finally expecting it, and had someone outside the vent stab through it.
Wonderfully subverted in a strip of Ctrl+Alt+Del, given that it LEADS TO THE DEATH OF THE MAIN CHARACTER! Thus ending this Gamebook storyline.
Nepeta is ordered by Equius to do this in Homestuck.
Later on, Gamzee also does this to creep on others.
And it's not like she was trying to rob the place or anything. She and another character, both recently hired there, show up to their opening shift and realize that neither of them have a key, on a day their boss is taking some personal time. Cue Raven's exceedingly well-crafted plan to get in so they could open the shop without bothering said boss.
Used again in another strip. Also justified, since it's done by Rudolph the Reindeer, who has picked up all the tricks Santa uses for shimmying up and down chimneys.
Banished: To escape from the Boscis base, Rak and Timbo follow a Mammazon out this way.
Charby the Vampirate: When Tony was cornered near a door he couldn't use inside the hunters' headquarters (since as an alp he can only leave the building the same way he entered it) he took possession of a rat monster to take the vents to where he needed to go.
Justified in Curvy when used by a native of Candy World who is actually a liquorice-based organism: she can squeeze into places a normal human wouldn't be able to. In fact, in the immediately previous page she's seen squeezing through the bars of a prison cell.
Averted in Dead Winter. Lou's plan for getting into the store for supplies involves this method, but Monday objects on the grounds that he won't fit. Apparently he's tried before.
In Drowtales, the air vents are too small for an adult Drow. But for a child...
In Girl Genius Castle Wulfenbach has a number of truly enormous grated vents which Gil uses to take Tarvek, Bang and Vole to one of his hidden labs when Tarvek figures out Gil's father has been wasped and is somewhere on the ship covertly giving orders. Gil notes that Tarvek really needs to escape since even if he's wrong about what has happened to the Baron the Baron would likely have him shot on sight.
In El Goonish Shive, Noah uses air vents in the process of hunting a magical creature, and the trope is discussed in the commentary. And Noah also does it to get around school! Raven has to shout at him to use the door.
In The Motley Two, the spaceship "Hiroja" has vents big enough that the characters can sneak around the entire ship with impunity. Perria Makara, who snuck aboard undetected, even sleeps quite comfortably in the vents (near the heating unit).
Lampshaded by the Deadpan Snarker in the improvisational comic The Omega Key on this page, where he finds it suspiciously convenient that he (a 6'10" man) can fit in an air duct. (He was right, as the destination turned out to be a trap.)
While it would appear to be justified in Star Mares due to ponies being smaller than humans (while the scale of the ships is unchanged from the originals, to better accommodate the larger ponies and pegasi), ventilation shafts are still explicitly stated to be designed for air, not ponies, and are depicted as being cramped and dirty. One character also later complains of the lack of security measures inside maintenance tunnels (which she is in the process of sneaking through).
Played with in Bob and George, where Kalinka and Ran try using air ducts to sneak into Wily's newest lair. Ran dies twice, trapping Kalinka in the duct, and necessitating that Blues show up to help her out of there.