"225. I will build machines which simply fail when overloaded, rather than wipe out all nearby henchmen in an explosion or worse yet set off a chain reaction. I will do this by using devices known as 'surge protectors'."
Battle Programmer Shirase's first arc (Episode 3) has Shirase destroying the King of America's computer through using a mobile phone to "double compile" the code, causing his computer to overheat and explode.
The second Digimon movie has the characters stopping the main villain on the Internet by redirecting a huge stream of email to the villain's address, causing it to slow down till it's frozen. Clogging a connection by sending massive amounts of data through it is at least a very realistic approach.
Also counts as a Chekhov's Gun since the same thing was happening to the heroes, who would have been able to beat Diaboromon from the beginning if millions of kids hadn't been constantly emailing them and clogging the bandwidth.
One Non-Serial Movie has a giant metallic energy-absorbing star as the evil Applied Phlebotinum device. Goku defeats this by overloading it with his own Super Saiyan energy, which causes it to explode in a chain reaction.
Goku defeats the light-eating monster Yakon in the same way, feeding him with energy until he explodes.
In the second season of the anime adaptation of A Certain Scientific Railgun, Protagonist Misaka Mikoto uses her Electromaster power (basically the ability to generate and control electricity freely) to remotely destroy several laboratories from a phone booth using the phone lines by hacking into their networks with her power, then wiping all data and critically overloading all the equipment, blowing them up and confusing the scientists as to why the hell all their stuff started randomly exploding.
F-Zero: Black Shadow's doomsday device is overloaded by driving around it in circles. The resulting explosion can be seen from a view of the galaxy.
In Doomtown, Hot-Loaded Rounds lets you boost a weapon bonus for one round of a shootout, after which the weapon is destroyed. But the destruction is tied to comparing poker hands, so if you win the shootout before it gets that far, then you get to keep the weapon. Particularly obnoxious with a Shotgun.
In Yu-Gi-Oh!, there is a Spell Card called Limiter Removal. The card doubles the attack of machine monsters but with the drawback of destroying them at the end of the turn.
Dr. No: James Bond overheats a nuclear power plant so it blows up and ruins the Big Bad's plan. It seemingly doesn't matter that it would cause serious environmental damage. It is James Bond, after all.
This is what the Hulk does to the Absorbing Man (natch) in Ang Lee's 2003 Hulk movie. Ew.
In Iron Man, Tony instructs his secretary to overload an Arc Reactor by "opening all the circuits and overriding the safety protocols". This remarkably simple exercise results in a massive electrical arc that shoots up to the sky.
Godzilla's "Nuclear Pulse" involves him overclocking his own body with radiation and unleashing a shockwave.
Are You Afraid of the Dark?: In "The Tale of the Virtual Pets," one girl tries to destroy the invading aliens' computer before they can upload her friends to their spaceship by running too many applications at once. It almost works, but the computer magically reboots.
In "The Sontaran Stratagem" the Doctor confuses a Sat Nav that wants to kill him with a Logic Bomb and it explodes... in a fairly small-scale and unimpressive way to which the Doctor responds disappointedly "Is that it?"
In "The Mind Robber", a computer was destroyed by people hitting lots of buttons and giving it too much to do at once. Well, either the computer was destroyed, or it was unable to perform various important functions that stopped it from being destroyed.
Also, as nearly done in "The Menagerie", hand phasers can be set to overload and cause a huge explosion. This is a deliberate feature.
In the Prequel Series Star Trek: Enterprise, the crew installs "Phase Cannons" (read: clumsily named proto-phasers) when they are beset with an enigmatic and superior alien attacker. In testing, a virus in the system caused the phase cannons to overload, obliterating a mountain used as a test target. When the standard settings of the phase cannons don't work against the alien ship, Archer orders Malcolm to deliberately overload them again and the phase cannons finally give the aliens something to worry about.
In Smallville, Bizarro is killed by Clark this way. He gives Bizarro a chunk of Blue Kryptonite. Just as Blue Kryptonite nulls Clark's powers, it overloads Bizarro's powers, causing him to explode.
In Andromeda, the High Guard's Force Lances can be set to overload and used as a grenade. This is a built-in feature.
In the Worlds of Power book about Blaster Master, the heroes stop the Doomsday Device by frantically pressing random buttons on it until it's overloaded and shuts down.
The Elder Scrolls IV: Oblivion: In the Shivering Isles expansion, the obelisks that summon the minions of the Big Bad can be powered up by inserting the crystal hearts of said minions. The only way to destroy an obelisk and prevent more minions from being summoned is to overload it by inserting several hearts in succession. It is something of a subversion, as the Obelisks don't blow up when overloading — they simply turn off. Looks like someone remembered the surge protectors.
In Advance Wars: Dark Conflict/Days of Ruin, you win the last mission in the campaign by destroying five laser cannons attached to a laboratory, causing the whole thing to overload and destroy itself, killing the Big Bad in the process.
During the climax of Resident Evil 5, the heroes discover that the source of Big BadWesker's insane powers is a virus. They also discover that the virus is unstable and must be injected regularly in precise doses, so their grand plan to defeat him amounts to overclocking him by injecting him with copious amounts of it. It doesn't do anything but make him angry. It also hideously disfigures him. If he somehow survived, the next time we see him he'll be a crispy mass of tentacles with Cool Shades.
An attack similar to the above example can be performed in Arcanum with a Fortifier chemical, which temporarily increases your damage resistance, but the withdrawal takes away a chunk of your health, and overdose cancels the positive effect and causes immediate withdrawal. You can make lots of it and inject several into enemies during a fight, causing significant damage each time. Note: do not give this to your followers or they will attack you.
Aera in Vega Strike use Photon Emission on Shield Collapse warheads. That's right, they weaponized "shield flash on hit" effect — a Photon autocannon shell or Photonswarm rocket is capped with an overloaded shield emitter, which fails when runs into anything, delivering both massive damage of a disruptor (shield like weapon) and a shield-piercing laser flash at point blank. Each shot consumes energy needed to charge the warhead and deteriorates with range, but less than disruptors, and it's still more energy-efficient than lasers.
The Overload and Sabotage talents in the Mass Effect series, the former downs shields and damages synthetics while the latter overheats weapons and burns the wielder.
Also, a rare human example. Zola imbibes some of Violetta's Moveit 11, making her extremely fast and strong. This, in addition to her considerable martial art skills, makes her completely unstoppable. Violetta's solution? Inject Zola with even more Moveit 11, so that her body can't handle it and melts down. Unfortunately for our protagonists, Zola managed to keep herself long enough to still wreak some damage. She's badly beaten by Tarvek, but she ends up in a hospital and is saved before Violetta's plan works.
Second Empire; Anzollo, knowing the Millennium Thargon has no hope of outrunning the attacking Dalek saucers, instead blows the gravity lenses of the Thargon to release a crippling gravity wave, which succeeds in tearing apart many of his pursuers.
Used by the Big Bad against the hero in Ben 10: Vilgax manages to remove the Omnitrix with a simple overloaded pulse of energy bigger than its feedback pulse.
In Chip 'n Dale Rescue Rangers episode "Pied Piper Power Play" the team destroys Nimnul's rodent-powered generator by convincing the mice to constantly run the treadmills. The twist is: the explosion would kill them all, as well as all the Nimnul's hostages, so they have to stop it afterwards.
The pilot for Darkwing Duck does this - to destroy the Waddlemeyer Ramrod, a device that "makes things float and stuff", the titular hero starts randomly pushing buttons, causing it to start firing randomly and finally explode.
Ron: This is a precision instrument, very complicated. Better mess with everything.
Sonic Sat AM: Sonic has been known to do this from time to time.
Static Shock: Gear stops Brainiac, the living computer brain that has invaded the Justice League's Watch Tower, by linking his computer/robot to it and downloading the same song billions of times — "just like when my computer crashes when I try to do too many things at once." It only appears to work, though.
Teen Titans: In the episode "Wavelength," Cyborg destroys Brother Blood's underground base by "boost[ing] the wavelength in the transmission matrix, triggering a meltdown in the amplification system." Which is funny, because increasing a wavelength will result in a loss of energy, instead of an increase.
Also, in the special episode "The Lost Episode," Beast Boy taunts a guitar-shredding villain into overloading his guitar amps by turning the volume up to ten.
Wallace & Gromit: In "A Close Shave", Shaun the Sheep tries to shut down the Conveyor Belt-O-Doom by randomly flicking a panel of switches. It doesn't work, but it does turn on a huge neon advertising sign outside so Gromit realises where they are and flies to the rescue.