Cliches you'd like to see subverted

*Sherlock *subverts this by just flipping the off switch.

Speaking of which, I’d love some smarmy Sherlock type detective finger the killer through a series of casual observations and brilliant deductions, only to be totally and thoroughly wrong. The real killer is caught and arrested by the local plod, who discovered them by, you know, doing police work. Gathering evidence, building a case, following proper procedure.

Something close for you, from Fear City (1984). (Spoilers, probably)

I just read a book where two FBI agents–one deep in the mystery, one new to it–were chased out of a basement by a bunch of corpses that got to their feet and shambled after them, led by a corpse that had clearly undergone an autopsy (the coroner who’d performed it was on hand and stated she’d removed the brain). Later, the experienced FBI agent mentions ties to voudoun legends, and the rookie is all, “Voodoo, really, you expect me to believe that bullshit?”

Yeah, actually, I do: YOU WERE JUST CHASED BY ZOMBIES. This isn’t the time for reflexive cynicism, lady!

Isaac Asimov did this in A WHIFF OF DEATH, when the ‘brilliant amateur sleuth’ protagonist gets told that all of his observations and deductions (a) prove nothing, and (b) if anything, support a weak case against him. The unimaginative local plod agrees that our hero has nothing conclusive, but does so with so stupid a comment that it prompts the real killer to incriminate himself – at which point the cop drops the Columbo act, having gotten the win by tripping the guy up.

Heroes are stuck in a room with no obvious means of escape. One gets the idea to open the ventilation duct, grabs a flashlight and pokes his head in there. “Nope, can’t do it. It’s too small, won’t support our weight, and has turns.”

Computer whiz searches for something online. He uses a mouse. Computer does not beep and boop. He discovers that he can’t find floor plans for the bad guys’ lair online.

Computer whiz wants to hack into bad guy’s system. He guesses at the password, is wrong, and gets locked out.

Cop finds bag of unknown white powder. Hands it to a colleague with a test tube of solution that turns blue when cocaine is added to it. Without putting a grain of the unknown powder in his mouth, cop confirms that it is cocaine.

Really? I think this subversion happens often enough that it has itself become a cliché. Though to be fair, the Sherlock character is usually proven wrong by someone else immediately pointing out some rather obvious incriminating evidence he overlooked, rather than a long period of careful, conventional police work.

Hero is sneaking into the bad guy’s lair, throws a knife at a guard and it hits him hilt first.

Hero cop is taken off the case and suspended so he goes home and reflects on his methods, concluding that following procedure would actually be the best way to solve crimes and afford him better career growth.

Villain is caught and taken to jail at the end. He doesn’t die in a hail of bullets, he doesn’t blow up on top of a building or fall to his death or crash into the ocean or have a semi truck fall on him. He just gets arrested and hauled away.

The military, shadowy government agency, or secret government cabal doesn’t have some evil super secret plan to take over everything.

More specific than a cliche, but still…

Scrooge: Boy! What day is it?

Boy: Why, it’s Boxing Day, o’ course!

Scrooge: Ah, shit! [Scrooge goes back into his house, slams the door. In the spring, neighbors report a strange smell coming from Scrooge’s apartment.]

The Manic Pixie Dream Girl trope (e.g. Garden State) where instead of fairy tale true love, a few years later, they progress to the more likely outcome of an insane dysfunctional train wreck.

The Dark Knight

Close to this is the Twilight Zone (1985) Season 1 Episode 13 segment “But Can She Type?”.The miserable secretary Karen Billings comes across a copy machine that transports her to another world. She is shocked to find people respecting her work as a secretary. She briefly returns to our world, only to realize that staying in a miserable world is stupid. The last scene has her being chauffeured to work in the world where secretaries are adored and honored.

Personally I like Phineas and Ferb where the villian has the most ridiculous backstory of all time.
“I was raised by Ocelots.”
“My father made me stand in the garden and be a lawn gnome.”

No moralizing sidekick, but subversion of the trope where the Good Guy can’t kill or he’ll become bad - Firefly Season 1 Episode 1 “The Train Job”[spoiler]Mal: Now, this is all the money Niska gave us in advance. You bring it back to him. Tell him the job didn’t work out. We’re not thieves. But we are thieves. Point is, we’re not takin’ what’s his. Now we’ll stay out of his way as best we can from here on in. You explain that’s best for everyone, okay?

Crow: Keep the money. Use it to buy a funeral. It doesn’t matter where you go or how far you fly. I will hunt you down, and the last thing you see will be my blade.

Mal: Darn.

{Kicks Crow through running engines. Next bad guy is brought forward}

Mal: Now, this is all the money Niska gave us in advance…

One of Niska’s Soldiers: Oh, I get it! I’m good. Best thing for everyone. I’m right there with ya.

Link[/spoiler]

The first half of this (Sherlock being totally wrong) was done brilliantly in a Flashman short story Flashman and the Tiger - which was based on the Sherlock story “the empty house”.

Flashman’s granddaughter is being blackmailed by Colonel Moran, so Flashman resolves to murder him (he normally avoids anything so violently heroic, but Moran threatens his granddaughters honour) - and disguises himself as a bum to commit the crime. He doesn’t need to go through with the killing, because Sherlock catches Moran - but he’s caught at the scene (he feigns drunkenness).

Sherlock proceeds to make a series of brilliant, but totally wrong, deductions about the “bum”, while the plodding Watson (correctly) identifies him as Flashman - but Sherlock convinces Watson he’s wrong!

[The kicker is that Flashman was gulled into protecting his granddaughter because he thought she was an unsullied pure type - only to find out that the reason his granddaughter wanted Flashman’s help was to protect the fact she was having an affair with “Beastly Bertie”, the heir to the throne! Flashman ruefully - but happily - concludes his granddaughter has inherited his own sensual, manipulative character].

Close to this is the Twilight Zone (1985) Season 1 Episode 13 segment “The Star” based upon Arthur C. Clarke’s The Star (It’s odd that two of your plot requests are somewhat examined in the same Twilight Zone episode - da [sup]di[/sup] da [sub]da[/sub]…)[spoiler]A group of space explorers from Earth return from an expedition to a remote star system, where they discovered the remnants of an advanced civilization destroyed when its star went supernova. The group’s chief astrophysicist, a Jesuit priest, is suffering from a deep crisis of faith, triggered by some undisclosed event during the journey. The final paragraph of “The Star” reveals[spoiler]the deepest root of the priest’s pain. Determining the exact year of the long-ago supernova and the star system’s distance from Earth, he calculated the date the emitted light from the explosion reached Earth, proving that the cataclysm that destroyed the peaceful planet was the same star that heralded the birth of Jesus. The scientist’s faith is shaken because of the apparent capriciousness of God:

Oh God, there were so many stars you could have used. What was the need to give these people to the fire, that the symbol of their passing might shine above Bethlehem?[/spoiler][/spoiler]

Showtime

William Shatner: [advising Trey on how TV cops taste drugs] You spear the knife into the bag… then pick some of the drugs up with the knife… then lightly press it on your tongue. And that is how TV cops taste drugs!
Detective Mitch Preston: What if it’s cyanide? There’s a reason real cops don’t taste drugs.

The police captain calls in the talented cop who doesn’t do things by the book…

Captain: Give me your badge and gun.

(The cop reluctantly does so)

Captain: Here’s your new badge and a better gun. You’re promoted! What, did you think we were gonna make you sit at a desk? You solve half the crimes in this precinct! If I took you off the streets, I’d be demoted within a week!

Here’s a scene I’d like to see…

Set-up: Two characters, let’s call them Bill and Mary. (More often then not, the “Mary” in the scenario is the love interest to the “Bill.”) Bill has performed some bone-headed stunt that will have unintended, BAD consequences for Mary. It hasn’t happened yet, but the dire consequence is imminent. Bill know it will happen, but Mary does not.

Mary is putting on her coat and is about to walk out the door.

Mary: “Well, I’m (off to work/going to the interview/on my way to my parents/etc.)”

Bill: “Ummmm…Mary. There’s something I have to tell you.”

Mary stops everything, and turns to face Bill, flashing a big smile, waiting.

Mary: “Yes, Bill? What do you want to tell me?”

Bill: (After a looooooong pause) “Nothing.”

Mary: “What? No, seriously what is it? Obviously, SOMETHING is on your mind. Come on, tell me!”

At which point, Bill confesses everything. Mary is upset, but understands that it was an accident and appreciates that Bill had the guts to tell her ahead of time so that she can brace herself and perhaps head off whatever shit is about to come her way. There is no scene later on in the movie where Mary screams “Why? Why didn’t you tell me???”

Law & Order, as in the entire (original) series subverts the “brilliant deduction” trope - just about every episode’s first half is exactly what you describe in your second sentence.
*Briscoe: “There was a pizza box at the scene - the pizza was untouched, like it had just been delivered. Maybe the delivery guy knows something.”
Van Buren: [wearily] “All right, start calling the pizza places in the neighborhood.”
[Briscoe and Green, looking really unenthusiastic, walk over to their desks.]

<cut - presumably to some time later - Briscoe and Green still hunched over their phones>

Green: [smiling] “Lennie! I’ve got a hit! That pizza was from a place 3 blocks away, and delivered between 7 and 7:30. I got the delivery guy’s address!”
Briscoe: [grabs his coat] “Let’s go.”*
I’ve long thought that showing this kind of police work was one of the secrets to the show’s incredible popularity and longevity. It’s comforting, in a way. We all know that if we or someone close to us is the victim of a horrific crime, the chance of getting a Sherlock on the case is zero - and L&O reminds us that we don’t NEED a Sherlock. Lennie Briscoe can find the killer just fine - and he’ll be more likely to have followed the proper procedures that will lead to an actual conviction too.

Well, unless you happen to be watching Law & Order: Criminal Intent, in which case the chance of getting Sherlock and Watson on the case is exactly 50% (for seasons 5–9) or 100% (for seasons 1–4 and 10).