Searching the Stalls

A character hides inside a bathroom stall, and to find him, another character enters the bathroom and begins a systematic search of each stall. If it's our protagonist hiding from the villain, then four things may happen (and none of these count as subversions!).

The villain gets interrupted before he makes it to the hero's stall.
The hero somehow escapes unseen and his stall is revealed to be empty.
Less commonly, the hero surprise attacks the villain before his stall is opened.
If the villain is Dangerously Genre Savvy and armed with a gun, he'll shoot into each stall, though the hero will likely find a way to avoid getting shot up.

Who is searching for whom varies widely, but it always involves a linear process-of-elimination search of the stalls. Expect a shot at foot-level at some point, and a Scare Chord when the last stall door is flung open. Variations on the basic structure are quite common.

Examples of Searching the Stalls include:

Anime and Manga

In Gunsmith Cats, May drags an injured Rally into a bathroom to hide from Radinov. Played straight despite Radinov not checking the stalls because of the obvious blood trail. She is, however, dealing with Minnie May now.

Comic Books

In the The Punisher storyline "Suicide Run", a bunch of mafia Mooks hide in the bathroom. The Punisher is not sure which stall contains what, so he shoots through all of them.

Film

Monsters, Inc., when Boo and Sully are hiding from Randall. He punches them open one by one, and Sully flinches as every door opens. Randall actually slams open the stall Sully is hiding in, but isn't looking at the time. Momentum closes the door before Randall sees them.
Nine to Five: Happens during an Imagine Spot.
In The Sting, Johnny Hooker is trying to escape a hit man trying to kill him. He goes into a restroom to hide. The hit man enters and starts opening doors to find him. He gets to the last stall and realizes there's a woman inside. He figures Hooker went out the window and does the same. It turns out Hooker was inside the stall with the woman—she was helping him.
In The Warriors, the Punks line up to kick all the stalls open at the same time. The Warriors open the doors first and a brawl ensues.
Max Payne: In the movie trailer, Max Payne does this using his gun.
The Amish kid in Witness successfully hides from the murderers this way.
Cast a Deadly Spell. As Mickey is trying to escape Tugwell in the train station, he goes into the bathroom and tries to hide in the last stall. Tugwell uses a magic spell that lights a fiery trail to him and blows him out of the stall.
Edge of Darkness. Craven is being followed, and to lose his tails he goes into a highway rest stop bathroom. A moment later the tails enter the bathroom and search the stalls, only to discover that Craven has escaped out a window and lost them.
Zombieland. Our hero has to relieve himself, and to be on the safe side, he searches each stall in the bathroom before doing so.
True Lies. Tasker hides from a gun-wielding terrorist inside a bathroom stall. The terrorist hoses down the stalls with his machine gun, and begins opening each stall. Before he gets to Tasker's hiding place, Tasker bursts out of his stall and escapes.
One Crazy Summer: The leader of a biker gang opens each stall and finds the person he was looking for in the last one.
High School Musical used this to show us how Gabriella was able to turn invisible. Seriously: Sharpay hears her singing in the loo, sees nobody, checks out the stalls, kicks the lone closed-yet-vacant stall open, then spies herself in the mirror and leaves. Gabriella then reveals that she was behind the entrance wall (beside the basins). In a place Sharpay looked. True, we don't actually see Gabriella's hiding place (so she could very well have been under the basins), but the way it's played makes us wonder why she doesn't slip out while Sharpay's back was turned.
In Air Force One, while he's being pursued by the terrorists through the plane's passenger levels, the President hides in the bathroom section. The terrorists then shoot up each stall, and check each door, only to find they're empty. Turns out the President used a different method to evade them.
In Pink Floyd The Wall, Pink is found hiding in a bathroom stall after the Hammers overrun England.
In Problem Child 2, Trixie hides in the bathroom and stands on the toilet seats so her feet don't show. Junior looks underneath each stall, and doesn't see her feet, but he isn't fooled.

Live-Action TV

In the Doctor Who episode, Partners in Crime, it turns out that the bad guys are actually searching for a different person, also a spy, who happens to be in the cubicle next to Donna's.
Battlestar Galactica: This situation occurs during a hostage crisis in season 2, at least, until Lee Adama jumps the guy supposedly hunting him from behind.
The Secret World of Alex Mack: Alex Mack once avoided detection this way, when her stall was opened for examination, she had liquefied and hidden in the toilet bowl.
Law & Order: UK: While pursuing a suspect through Waterloo Station, DS Matt Devlin realizes he must had fled into the bathroom to hide. When he goes into the bathroom to look for him, he doesn't even need to search the stalls—only one has the door closed.

Video Games

Grand Theft Auto IV has a mission where a guy you're chasing runs in the bathroom. You have to open stall by stall to get him.
Punisher (2005): A male mook sometimes will try to hide in the women's restroom (at Central Park Zoo). Doesn't work out, as Frank can explicitly drown him in the toilet. That's going to give a tourist a scare.

Western Animation

The Simpsons. To paraphrase, "I've never seen anyone so desperate to avoid ten minutes of calisthenics".
The Venture Brothers. Brock is looking for Phantom Limb inside a bathroom. He begins searching each stall, encountering a different villain in each one, before finding his target.

Other

There's a Japanese Urban Legend about Hanako Of The Toilet, a schoolgirl murdered in a bathroom stall who kills anyone who happens to be using that particular toilet. According to the story, if one is unfortunate enough to be using that stall, they'll hear Hanako herself checking each stall, giggling to herself "No one in here," until she finds the victim. Then she kills them.