In Saiyuki's "Kami-sama" arc, Sanzo attempts to break a barrier that he thought was created by will power by shooting at it, on the "rationale" that the bullets are infused with his will power, and thus the two will cancel out...yeah, no. Instead, the bullets ricochet back and everyone dives for cover, with Hakkai yelling, "What are you DOING, Sanzo??"
Yuna Roma Seiran gets this from the ORB military officers in Gundam SEED Destiny, for hiding war criminal Lord Djibril in ORB and denying it, then acting all surprised when ZAFT sees through his obvious lies and invades in full force. Apparently, he thought that since ORB had successfully hidden the Archangel from them two years ago, but not even in anime do politics bend to the Rule Of Cool...
In Full Metal Panic, Kaname tends to yell this whenever Sousuke does something insane. More often than not, he proceeds to explain the ridiculously complicated terrorist plot that he foiled to justify his actions. Sometimes the plot is even real.
From the Star Wars: Clone Wars comics, during the battle of Kamino:
Commander Merai: What were they thinking, defending a water world with ships that can't submerge?
The Goonies. Stef barks this at Andi when she hits the wrong notes on the musical lock, causing part of the floor to collapse.
Stef: What were you thinking? Andi: I hit the wrong note! I'm not Liberace you know!
Zoe Heller's novel Notes on a Scandal (later made into a film of the same name) was released under the (patently absurd, given the novel's tone) title of What Was She Thinking? Notes On a Scandal in the US.
Live Action TV
Elliot Stabler frequently hears this on Law & Order: Special Victims Unit: when he drove a paranoid-schizophrenic to a breakdown to get information, when he tried to convince the parents of a girl beaten up by his friend's son not to testify, when he made his daughter's DUI disappear, the infamous "What possessed you to tell the shrink in your psych evaluation that you fantasized about killing suspects?!" Or the time when he told the father of a murdered girl that the Suspect might get away with it...
Captain Cragen also said this to Olivia Benson when she gave a reporter confidential information about an investigation involving Anthrax.
Fin Tutuola heard this from John Munch and his ex-wife in the episode when he handled a case against his son poorly.
Adam Schiff does this to Jack McCoy when he cuts a very favorable deal for a mob hit man in "House Counsel" because he wants to beat the mobster's attorney, who happens to be an intense rival of McCoy's from law school.
Schiff: What are we running here, Benny's Bargain Basement? Today's special - cop to four murders, and serve only five years.
McCoy: I didn't think-
Schiff: You didn't think because the blood was too busy rushing from your brain to somewhere south of the border!
A lot of people screamed this at Mohinder from Heroes when he injected himself with a Super Serum he'd invented mere hours ago from studying a woman who cries death, while outside in a bad part of town. And also wanted to distribute it to the general public, despite the fact that a remarkable proportion of those with powers kill people a lot or even try to destroy the world.
Used in an episode of Everybody Hates Chris, in which Julius is laid off and has to take care of the house, cooking, and cleaning while Rochelle tries to find a job. After being insulted by Rochelle for most of the episode, Julius makes the mistake of saying that taking care of the house, which Rochelle usually does, isn't that hard. Cue Rochelle, who is known for cursing people out, launching a positively horrifying hour-long tirade that had Julius cowering in the corner, ending with Rochelle yelling "HAVE YOU LOST YOUR MIND!??!"
Jay Leno famously asked Hugh Grant after the latter's sex scandal: "What the hell were you thinking?"
Denis Leary said the same thing about Marv Albert's scandal in his stand-up special, Lock and Load.
Late in the Band of Brothers miniseries, Easy Company passes some surrendering Germans traveling in the other direction, troops marching and officers on wagons. Webster leans out of a troop transport and starts berating them: "You stupid bastards, look at you! You have horses! What were you thinking?!"
For added irony, they are on the autobahn. The Americans in trucks on the road, the Germans walking the other way in the median.
Comes up quite a lot in WWE, either from skits backstage after a loss (or near-loss) because of a tag team partner, or when a commenter wonders what a high-flyer was thinking after attempting a high risk move successfully (or unsuccessfully) and losing the match.
Kane buried The Undertaker...again. He decided to hold a funeral in respect of him...and then Alberto Del Rio interrupted. Now, given that Alberto has only been on Smackdown for a few months, and Kane is a veteran who just took out The Undertaker, and that Alberto interrupted his "funeral" just to challenge Kane, the audience, Kane, and pretty much anyone else who may have been watching all exclaimed...
Some fans exclaim this when a promotion has a good angle or rivalry going and then proceeds to screw it up somewhere along the line. WWE tends to get this a lot. For example, dropping the US Title rematch of Daniel Bryan vs Sheamus from Wrestlemania 27, considering that they're two of WWE's most consistent workers and could have put on an awesome match.
Folk singer Christine Lavin's song "What Was I Thinking", originally written in the late 1990s, features such examples as a poor choice of formal dress, hair style, and poor choice of White House intern.
Zits has Mom convey an expression that says this phrase without using words to react to Jeremy's antics. Likely she doesn't say it because Jeremy will likely react with some quip.
Mom: What were you thinking! Jeremy: Everything's cause-and-effect with you, isn't it.
Take an RPG, any RPG, and one character will inevitably say this to another.
Neither has brought anything to review, so Brad is looking at a clothes iron held by Phelan
Phelous: Um...clothes...wrinkly... Cinema Snob: Doesn't look to terribly b- He reaches out and touches the plugged in iron Cinema Snob: OW! FFFUCK! Phelous: ...did you think would happen?
Spoofed in the Ed Edd N Eddy episode "Cry Ed", where, after Ed drops a house on Eddy in response to Eddy's scheme to get himself injured and gain sympathy, the following exchange occurs:
Edd: Ed! What in heaven's name were you thinking?! Ed: Absolutely nothing, Double-Dee.
Avatar The Last Airbender: Zuko frequently hears this from his uncle- "Of all the foolish things you've done in your sixteen years, Prince Zuko, this is the most foolish!", "You never think these things through!" In response to short-sighted things such as when he went through a great deal of life-threatening dangers to get the Avatar and would have died if Aang's friends hadn't come and decided to Save the Villain.
Apu: Oh, you have got to be kidding sir. First you think of an idea that has already been done. Then you give it a title that nobody could possibly like. Didn't you think this through... (timeskip fade) ... it was on the bestseller list for eighteen months! Every magazine cover had... (timeskip fade) ... one of the most popular movies of all time, sir! What were you thinking? (pause) I mean, thank you, come again.
Transformers Animated: Megatron kidnaps Bulkhead to complete his space bridge, and Bulkhead is so sick of people assuming he can't do anything that he makes it work. When Professor Sumdac calls him on this, Bulkhead points out that Sumdac was the guy who rebuilt Megatron (although he had no idea about the evil tyrant thing).