Anytime you hear the phrase "Joudan ja nai wa yo!" screamed (in Ranma ½, particularly by Akane) is basically this, as it literally translates into you "You've got to be kidding (or joking with) me!"
Ghost in the Shell: during the Tachicomatic Days section of episode 3 of Stand Alone Complex, the Tachicoma utters this when it looks up to see a huge tank about to land on it.
Ryuuji in the Festival Arc of Toradora!, when he finds out Taiga's father won't be coming to see her in any of the school's activities.
Naruto: the titular character and Sasuke say this in a filler episode when they see Kakashi is wearing a mask even on hot spring.
Crocodile from One Piece uses this phrase after witnessing Luffy's idea to fight him, which included him swallowing a barrel of water to protect it since water is the only thing that can actually touch Crocodile at the time.
Then there's a more comical example in the Skypiea arc. Faced with a choice of four doors, Luffy says after they've entered that it may be like a game; pick the right door, you get a prize, and pick the wrong one..."then you fall off the island". Usopp panics, as the island they're on is 10,000 meters in the air, and Sanji dismisses it as absurd. Then they reach the end of the tunnel...and find that while the other three paths go straight forward, theirs plunges straight down, out of sight beneath clouds. Amidst the Wild Takes, Usopp says this line.
In Legion of Three Worlds, this is Superboy-Prime's reaction upon discovering the 31st Century's Superman Museum.
In "In The Beginning", Frank has to fight Pittsy the mob enforcer for over a dozen pages. The nutcase manages to blow off one of Frank's ribs, then attempts to tear a lung out through the hole. Frank retaliates by throwing him out a fifth-story window onto a metal picket fence. Then jumping out after him and Goomba Stomping him, driving three fence spokes three inches through his torso. Two pages later, Pittsy not only manages to tear the fence loose, but goes looking for Frank with it sticking out of him.
Frank Castle: You have to be fucking kidding me. (Gives Pittsy a Boom, Headshot. With a shotgun. At arm's reach.) Next step's a reflex action. So's the next one. Got to be. (Gross-Up Close-Up of Pittsy's shotgunned face)
Pittsy of course dies, but the reader doesn't get to see if Frank had to shoot him again.
In "The Long, Cold Dark", after Frank had captured his nemesis Barracuda, shot, beaten and electrocuted him* His balls, specifically, wired to a car battery. For over an hour. Well, Barracuda did kidnap and threaten Castle's infant daughter hoping to piss him off enough to put up a good fight - Be Careful What You Wish For, indeed. and left him wrapped in iron chains in the boot of his truck while he attended to other matters. It's all too much for 'Cuda, who just snaps, breaks the chains through sheer strength and barrels out.
The Punisher: "You have got to be fucking kidding me." (Barracuda arms himself) ...was the thought that came to mind.
The Thing (1982): Also doubles as a moment of levity in an otherwise horrific scene, in which the Thing-mimic of Norris detaches its head. Made even funnier when you realise later that Palmer, the man who uttered the line is also a thing!
In From Dusk Till Dawn 2: Texas Blood Money Robert Patrick managed to cram even more profanity into the phrase when a total eclipse of the sun makes containment of vampires in a bank during the day impossible.
The Fugitive: Gerard and his men have cornered Kimble in a tunnel, blocking both exits. But he doesn't attempt to come out of either exit, he's not in the stolen ambulance he was driving, he's not hiding in any of the other cars in the tunnel, he appears to have completely vanished into thin air, leaving the marshals incredulous, and Bobby Biggs outright states "You've gotta be kidding me!" Until Gerard hears the sound of trickling water and follows the path to a storm drain and he (and the audience) realize that this is where Kimble has fled, and tells them they've got a gopher.
In the Star WarsExpanded Universe book Enemy Lines 2: Rebel Stand, Han and Leia are trapped in prison, awaiting what looks to be their final meal before they're shipped off-system to the Yuuzhan Vong. Instead of breakfast, Han's blaster, Leia's lightsaber, and an assortment of other useful items pour through the food tray slot courtesy of a complex plan by R2-D2, and the obligatory line is Han's reaction.
Also, when the Ninth Doctor ends up on a futuristic version of Big Brother, "You have got to be kidding."
The protagonist of the US remake of Life On Mars gives a quiet "No way" upon waking up in the 70's and seeing the World Trade Center still standing.
John Crichton on Farscape, more than once. Not always very sensibly either: once he says "Aeryn, honey, you have got to be kidding me" on the discovery that she objects to serious drug abuse. And no, he wasn't being sarcastic.
The Office: Kevin reacts this way to Jim's declaration that he's single and Pam saying that they're "good friends" at the start of season 4. He's right.
Wire in the Blood (TV special): Dr. Tony Hill literally says this when set up and busted for possession of cocaine in his car (after he has pried around too much for the Texas locals). Unusually, everyone else, including the cops, also acknowledges how ridiculous the charge is, but they go through with the drop-charges-if-you-buzz-off-now spiel nevertheless.
Burn Notice, 5x10, when a duped bad guy sees Michael, out of cover and alive.
Final Fantasy XIII: Lightning summoning Odin for the first time cues the following quote just before he tries to bisect Hope. Bonus points for snarking her sudden role as the Badly Battered Babysitter after they were separated from Sazh and Vanille prior to the summoning.
This cannot be happening.
Variations happen twice in Modern Warfare. First, when Gaz hears that The Squad's extraction point has just become compromised and they have to fight through a virtual army downhill to the secondary one before the chopper leaves without them, he lets out the anguished: "Oh, he's gotta be taking the piss!" A few levels later, Price, Soap, and Griggs fight their way to the final bunker door under extreme time pressure and the door begins to open veeeeerryyyy slooowlyyy. Griggs: "Oh, you gotta be shittin' me!" Cue snarks from Price and Gaz on the comms. In Black Ops Hudson says the quote verbatim when told the only way to escape a pursing Spetznaz hit-squad that wants him, his partner and their prisoner dead is to jump off the roof of the building they're all standing on.
In the very beginning of Beyond Good & Evil the main heroine Jade finds out that the power company cut off power feed to her house for nonpayment. Oh, yeah, she finds it out when the defensive force field over her house dies in the middle of an alien invasion. Jade is apparently a very polite and temperate girl so the worst she has to say over the situation is You Have Got to Be Kidding Me!.
Shepard utters this exact line in Mass Effect 2's Overlord DLC when the huge satellite dish they just disabled starts collapsing. While they're still standing on it.
James: (as the party runs towards it) You've got to be kidding!
The Uncharted series uses this at least once per scene. Often said by rogueish protagonist Nathan Drake as he suddenly finds himself face-to-face with a tank, or a helicopter, or a slimy zombie-like thing, or a dude with a humongous gun. Or even just another wall that must be scaled.
Zidane of Final Fantasy IX says this almost word-for-word when the Armodullahan appears out of nowhere in an enclosed space. To his credit, he does start running before saying the line.
In the MGS3 Secret Theater Video, Metal Gear Sigint, Naked Snake ( aka Big Boss) says it at the end after Sigint gets the Big Boss rank from President Lyndon B. Johnson.
In Metal Gear Rising: Revengeance, Raiden says this exact phrase right before the final boss powers up. Odds are the player will say the same thing at this scene.
Kyle Katarn in Jedi Knight, when he sees just how far he's got to jump to get to his goal. The player probably had a similar reaction: it is a long way over a hell of a drop.
In Killzone 3, after blowing up an oil rig and jumping to safety, the resulting wave towers over him, and he simply quips "...really?"
Both AWACS Thunderhead and one of the allied tanks in Ace Combat 5 have this reaction in the "Desert Lightning" mission, after the enemy manages to sneak a battleship into the river near their fallen airfield.
Sheena in Tales of Symphonia is very fond of this line when she gets flustered, such as if Lloyd catches her playing with children and Luin and comments how cute this makes her look.
It's also what she'll say if an enemy lands a critical blow on her in battle.
Mr. Sandman's Title Defense in Punch-Out!! Wii upon seeing Little Mac has taken not only his title, but also his fans.
Chorocojo had a similar reaction after finally managing to catch a Weezing in Crystal, wasting a ton of Ultra Balls on it before finally catching it with a Great Ball (made funnier considering Great Balls had literally never worked before that point).
In The Mercury Men, words to this effect are said by Edward on several occasions.
In the pilot episode of Danny Phantom Sam is trapped by a ghost in a pile of meat. She utters this line when Tucker arrives with a knife and fork, assuring he'll free her in no time.
This is Tak's verbatim reaction in Invader Zim when Zim, instead of figuring out that she's a rival Irken who's out to prove herself a better invader than him, concludes that her mistreatment of him over the past several days meant they were dating, and so triumphantly "breaks up" with her.
Avatar: The Last Airbender: Aang overcomes a Fire Nation vessel with some difficulty... then says this exact phrase on seeing the ENTIRE FLEET behind it!
In the Teenage Mutant Ninja Turtles 2003 cartoon episode "Scion of the Shredder", Raph has tired himself out fighting a few Foot Soldiers while escaping on an elevator. Then, just when he's catching his breath, more Foot Soldiers show up. His response? "You've gotta be kidding me."
This isn't the only moment he drops this - he says it quite often when he runs into trouble. For example, he even dropped it at least once in the Fast Forward episode "Home Invasion" when a machine that brushes his teeth and puts shaving cream on his face came to life where he thought he could get the privacy to read a newspaper.
In the Batman: The Animated Series episode "Beware the Grey Ghost", Bruce Wayne realizes that a series of bombings are copied from the Grey Ghost show he enjoyed as a kid. After the actor who played him hands over the episode, which Bruce enjoys watching while searching for clues, until he finds out that the bombs were driven in toy cars, leading to a unbelieving reaction and Bruce to comment, well, You Have Got to Be Kidding Me.
In the Scooby-Doo, Where Are You! episode "Don't Fool With a Phantom," Fred accidentally encases Shaggy and Scooby in hot wax along with the Wax Phantom. When he chips them loose:
Fred: Okay, Scoob?
Scooby: You've gotta be kidding!
In the Star Wars: The Clone Wars season 5 episode "Bound for Rescue", Ahsoka has this reaction when she sees that the "Animal Instincts" are actually the younglings in disguise who came to rescue her from Hondo Ohnaka (though she says it as "Oh no...").
Notably, the unofficial catchphrase for Wild Weasel crews was "YGBSM", for "You Gotta Be Shittin' Me". To clarify, the Wild Weasels were Vietnam-era USAF fighter aircraft whose job was to act as bait for North Vietnamese air defenses, in hopes of drawing their fire, evading it, and then destroying the antiair site. The phrase was supposedly coined as
This is, by the way, still US Air Force doctrine when they cannot locate the SAM or AAA site through other means. It's called SEAD duty (Suppression of Enemy Air Defense), and pilots are typically not happy to draw the short straw on it.
The original Catch-22 revolved around this: aside from serious wounds, the only way to get out of flying a dangerous bombing mission was to claim insanity. Any airman who tries to get out of flying dangerous bombing missions by claiming insanity is clearly sane enough to fly them, because he's trying to avoid doing so.