Thermometer Gag

When a character is feverish and requires a thermometer, there will often be a joke about using it in an inappropriate orifice. This takes two main forms; either the thermometer is being used in the incorrect end, or it's being used in the correct end and the victim simply doesn't want it there. Subtrope of Toilet Humor and Ass Shove.

Examples of Thermometer Gag include:

Comic Books

A Futurama comic book involved Cubert being sick and complaining of how Doctor Zoidberg used the rectal thermometer rather than the oral one. Zoidberg did in fact use the oral one, but "had bad aim".

Film

There's a joke early in the movie Idiocracy in which the main character is given a brief examination. He's told that a specific probe that he just had in his butt is actually supposed to go in his mouth.

Live Action TV

In the Pilot episode of M*A*S*H, someone accidentally uses a rectal thermometer as an oral thermometer.
On House, Dr. House's first encounter with villain Tritter begins when House sticks a rectal thermometer up Tritter's butt and leaves it there for several hours.
Used as a threat in an episode of The Suite Life of Zack and Cody, wherein Cody warned his mom to stop talking with the thermometer in her mouth, "or we'll have to do it the other way."
Variant in the show ER: Garrett Morris plays a patient who annoys the staff so much that they finally make up a pretext to take his temperature—and then leave him with a sunflower up his ass.
In an interesting variation, one of the winners on America's Funniest Home Videos was a little girl who thought she was taking her temperature. Turns out what she'd taken for a thermometer was a used pregnancy test.

Newspaper Comics

Liberty Meadows: Leslie the Hypochondriac Bullfrog rushes into Frank's office claiming to be sick, and yanks the thermometer out of Frank's hand and puts it into his mouth to prove it. Frank tells him it's not an oral thermometer. Jeopardy Thinking Music ensues, and then Leslie spits it out.
In Get Fuzzy, Rob takes Satchel's temperature when he's sick, and Satchel wants to know why he's putting the thermometer in his ear. He knew it wasn't an oral thermometer, but apparently he'd been using it somewhere else...
One The Far Side cartoon has an image of a scientist with a giant thermometer approaching the backside of a dinosaur:

"An instant later, both Professor Waxman, and his time machine are obliterated, leaving the cold-blooded / warm-blooded dinosaur debate still unresolved."

Web Comics

Something*Positive: Davan refuses a rectal thermometer during a checkup and insists his temperature be taken via "the forehead, ear, or, and this may seem novel, under the tongue". The doctor responds with "Fine, but you're the first person to ask me to stick a rectal thermometer in his mouth."
Scandinavia and The World: When Finland gets ill, Sweden warns him they now only have two rectal thermometers because Denmark jumped the gun when told that was the best way to take temperature.

Western Animation

Madagascar: Melman presents Marty with "my first rectal thermometer" for his birthday and doesn't tell him where it's been until after Marty's had it in his mouth. Admittedly Marty, being a zebra, has no hands ...
In the same franchise as the above example, in The Penguins of Madagascar, Julien makes a comment about being glad he's not a mammal. Kowalski proves him wrong by checking various points of mammalhood, including warm blood. It's not really shown onscreen, but the Hammerspace thermometer and Julien's expression make it easy to guess how he does this.
An episode of The Fairly OddParents had Vicky become nice. After she checked Timmy's temperature, Cosmo remarked that she remembered to use the correct thermometer.
Done, of course, in The Simpsons when Grampa is looking after Bart in the episode "Marge Gets a Job".

"Oral thermometer, my eye! Think warm thoughts, boy, 'cause this is mighty cold."

An second season episode of Total Drama Island, One Flu Over the Cuckoos, does this. When everyone but Leshawna and Duncan are sick, Duncan attempts to put a rectal thermometer in Harold's mouth.