Yu-Gi-Oh! GX used the "arms too short" subversion when the Master of Oz monster battled an Ancient Gear Golem. At first the Golem was weaker than the Master of Oz, and it was a normal punch... and then another card doubled the Golem's power, and it delivered the Cross Counter, whereupon the Master of Oz's arm turned out to be too short.
Des Kangaroo's special ability could also be an example of this. While never seen in the anime, its effect is that if it's attacked by a monster with Attack that is lower than Des Kangaroo's defense, the attacking card is destroyed. This specific move is known as the "Destruction Punch", and there are other cards that grant its effect.
There's also the card "Gachi Battle!" which depicts two cards doing this.
Also, in Yu-Gi-Oh! 5Ds, one episode has Yusei and Jack getting into a fist fight that ends with one of these.
A comic featured in a magazine dedicated to the Digimon Wonder Swan games has Taichi Yagami and Ryo Akiyama give one to each other during a More Hero Than Thou scene. It was later reproduced as a bonus chapter for Digimon V-Tamer 01.
Dragon Ball has this as well, during the first fight with Goku and "Jackie Chun" (a disguised Master Roshi). The only reason Roshi won was because his leg was longer, so he was able to kick slightly deeper than Goku.
Dragon Ball Z has a straight example during the fight between Goku and Vegeta after he's become a Majin. Don't think about the fact that Vegeta should probably have shorter reach.
Or that since high-speed fighting is the norm for DBZ and fight scenes are meant to be very serious that the moment the trope is played straight it's accompanied by a few seconds pause and a cartoonish sound effect.
There's also a Like Father, Like Son moment where Goten and Trunks land cross counters on each other in exactly the same manner their fathers did.
In Death Note, L and Light Cross Counter each other during the Yotsuba arc, after Light tries and fails to convince L that he couldn't be Kira. L uses a kick to fulfill his end of the Counter.
Done by Ichigo and his dad in the first episode of Bleach.
In the third episode of Tengen Toppa Gurren Lagann, Simon and Kamina in their newly-combined ganmen (Gurren-Lagann) rushes towards Viral's Enki. Viral throws a punch, and Kamina throws a punch along the same line. When both ganmen's fists hit each other's faces, Dayakka yells out (in Gratuitous English), "CUROSSU COUNTAH!" and the shot takes on the same yellow hue with dark shadows as the punch from Ashita no Joe (as pictured at the top of the page). Another Cross Counter happens much later in the series, being the first attack that starts the Final Battle between the Tengen Toppa Gurren Lagann and the GrandZamboa.
Played for laughs in an early chapter of Shaman King, when Anna summons the spirit of swordsmith Mosuke into Ryu's body so he can fix Amidamaru's broken sword. At first, Mosuke is pissed at the fact that his handiwork's been damaged and rushes at Amidamaru (in Yoh's body), who also attacks him with the excuse that his old friend hadn't talked to him in about 400 years. They (Ryu and Yoh, technically) then do this to each other, before the spirits they're hosting smile and greet each other properly.
Anna: Men are so incredibly dumb. Looks like they can't even meet each other without acting flashy.
Done during a Filler arc by Luffy and Zoro in One Piece. The following scene has Chopper finding them, locked in the Cross Counter position, buried up to their waists in the sand... apparently they knocked each other out, but didn't fall down.
The cover for Chapter 366 has one between Dorry and Broggy, who were last seen continuing their endless fights against each other (always draws) with broken weapons.
Sanji and Mr. 2 Bon Clay do this to each other with kicks.
This happens again much later on, in the Fishman Island arc, between Luffy and Jinbe (And Sanji, who had stepped in between them and suffered both fighters' blows).
This is how the fight between Sakura and Ino ends in the Chuunin Exam arc.
A filler episode has a sparring match between Rock Lee and Naruto end in one.
Much later, one occurs between Naruto and one of Pain's bodies, although both avoid direct blows, which is good for Naruto as he avoids getting stabbed in the face and is able to blow the body away using the sheer natural energy from his Sage Mode.
Happens twice in a row in the second Fatal Fury OVA, during the final fight between Terry and Krauser.
Done many times in Pokémon. One instance is between May's newly-evolved Combusken and a Breloom. Seen here.◊
And Ash's Bulbasaur and Jackson's Meganium during the Johto League Silver Conference. Both examples were following two of the most brutal fights the show had ever seen. The Silver Conference fight's instance is this.◊
This happened repeatedly in Kidou Tenshi Angelic Layer. In the fight between Wizard and Hikaru, it was even altered so that, though Wizard was still punching her, Hikaru had kicked him in the face instead.
In Mousse's introductory chapter of Ranma ˝ Ranma tries to do this with a flying kick, forgetting that he was a girl with shorter legs than Mousse.
The comedic version is seen when he allies himself (briefly) with Pantyhose Taro:
Pantyhose Taro: Thank you, you swell cross-dressing guy! Ranma: Never mention it, Pantyhose Taro! Both: Don't call me that! (cue cross-counter with Taro delivering a straight jab inside Ranma's right hook)
Porco Rosso does this during the fight between Porco and Curtis.
The whole scene demonstrates that the two are really poor fighters.
A variation with fencing sabers was done at the end of Char and Amuro's Sword Fight in the finale of Mobile Suit Gundam. They rushed each other, Single-Stroke Battle-style, each delivering a thrust through the other's defenses. Amuro got stabbed in the shoulder, Char got stabbed in the (armored) forehead. This pretty much ended the fight (seeing as they each broke their swords in the process)...until The Movie, anyway.
Setsuna and Graham's battle at the end of Gundam 00 season 1 is pretty much the same, except that they're in their BFS-wielding Humongous Mecha instead of on foot.
The final battle of season two ends on a similar note with Setsuna and Ribbons going for a dual stab. Both their units are totally destroyed (GN drives and all) and Ribbons is killed, but Setsuna survives.
Another sword version in Gundam SEED Destiny during the Freedom's final moments: Kira managed to put a beam sabre through the Impulse's head, while Shinn ran the Freedom through with its anti-ship blade. Little wonder who won that fight, even if Kira did put the Impulse out of commission for a few episodes.
Though that was mostly due to Kira's no kill policy that he did that. He could have went for the chest instead, making it a double KO. Possibly a win since Kira ended up surviving anyway.
In the dramatic match between Pegasus Seiya and Dragon Shiryu in Saint Seiya's Galaxian Wars arc, the two combatants leap high above for some Air Jousting and end up locked in a Cross Counter —Shiryu's strongest punch on Seiya's face, Seiya's straight jab into Shiryu's Achilles' Heel (the Dragon's Claw over his heart.)
Kenshiro and Falco do a cross counter in Hokuto No Ken 2 anime when they fight.
Used in Shamo, between Ryo Narushima and Naoto Sugawara.
Genesic Gao Gai Gar and Palparepa cross counter during their fight in GaoGaiGar FINAL.
Arcueid and Ciel in Kagetsu Tohya. Neko-Arc, actually, which indicates how dire the situation is.
Happened in episode 71 of the Monster Rancher anime, ending the fight between Mocchi and Most in a tournament. Most, a more experienced fighter, was still standing, but Mocchi was knocked out, leaving Most the winner. Keep in mind this had followed a fight that had lasted the entire day.
Mahou Sensei Negima!has one, too. Fate shows us a nice way to avoid the problem of one's hand being shorter then the opponent's, simultaneously reducing Negi's hit from head-on to glancing. Counts as a variation of the trope, because the "counter" is not straight, but rather a hook.
In the manga webseries, Key to the Sky, Trisha and Meer perform a crosscounter on one another in chapter 15, however, neither of them are knocked out.
In High School D×D, Issei and Raiser pull this off in their one on one fight at the final episode of the anime/volume 2 of the light novel. Issei puked blood out of his mouth but Raiser didn't until a few moments later, shocking him in disbelief because he's a phoenix who can heal through any damage right away. Until he sees how Crazy-Prepared Issei is for such an occasion.
Speaking of, Kamen Rider has a variation that pops up from time to time where, instead of hooks, two characters will throw out front thrust kicks at the same time; often this is used to get some space between the characters so one (or both) can do something dramatic.
Robot Combat League: Crash vs Steel Cyclone had one of these as the climax, which ended in some nasty damage for both, though it was Cyclone that had the worst part, getting its arm wrecked.
There is an actual move like this in real life, but usually just called a cross, and much more effective. Assuming both boxers are right-handed, one goes for a front (left) hand jab, while the opponent uses the back (right) hand to cross the opponent's now outstretched left arm and connect with the opponent's head. If done correctly, it is an effective counter that will also protect the user from the opponent's jab.
It should be noted that in a real Cross Counter scenario, the cross would prevent the hook from landing (because it stuns the opponent and prevents them from completing the hook) unless it's really weak or really late; that's why Cross Counters are so rare in real life.
The rear-hand-hook-over-jab version is very popular in Mixed Martial Arts (Mauricio 'Shogun' Rua especially throws it with great success). The reason is poor striking technique among a lot of fighters (who mostly start as wrestlers): not tucking the chin behind the shoulder of punching hand and general focus in MMA on single punches rather than combinations (due to takedown risk Hit-and-Run Tactics work better), which means that a large number of jabs is usually thrown without any followup strikes (sometimes to set up a takedown).
Filipino wrecking ball Nonito Donaire is a master of this technique; after baiting Fernando Montiel into throwing a big right cross, Donaire countered over it with a monstrous left hook which left Montiel spasming on the mat.
A common routine sees two wrestlers both going for a clothesline on each other at the same time, ending up with a clothesline version of this trope. How much damage this accomplishes varies depending on the type of match: a normal, unimportant match might just see the wrestlers go down for a few seconds, while a "Last Man Standing" match (the sole objective of which is to keep your opponent down for a 10-count) or a heated title bout will inject some drama into the match up by having the wrestlers stay down for much longer as they struggle to get to their feet before the 10-count. A less-common variation will see two (usually taller-than-average) wrestlers hit each other with Yakuza Kick/Big Boot-type moves at the same time. Similarly, many high-fliers use the Flying Cross Body - literally just running into a jump so that your body makes a cross with the opponent's and you drive them to the mat - but seeing two wrestlers do this simultaneously is not only a full-body version of the trope but looks more devastating than a car crash.
This is known in most fighting games as "trading hits." Usually leads to a Double Knockout (which counts as a loss if it's a complete draw match.)
Dudley from Street Fighter III has a move with this exact name, and it functions in the same way as well, only it's more of a blazing-fast dash punch than a straight up exchange. He does deal equal or close to equal damage to what hit him, though.
Sadly for Dudley, his Cross Counter will not result in a double KO ever, since if he's KO'd during the move, he'll hit the Counter... and immediately collapse in defeat, with the move doing no actual damage to his opponent.
See also the Street Fighter-centric webshow, Cross Counter, starring community darlings Gootecks and Mike Ross.
Done in Metal Gear Solid: The Twin Snakes. Liquid and Solid duel on top of a wrecked Metal Gear Rex, and end up in a Cross Counter.
This is then repeated in a much more satisfying way in Metal Gear Solid 4 where during the final fist fight with Liquid Ocelot, one of the many context sensitive actions the player can pull off is a Cross Counter.
One of the Quick Time Events in Metal Gear Rising: Revengeance when fighting the final boss ends in one, although there's no outcome where both the boss and Raiden get hit: if you succeed in the QTE, Raiden evades the boss' punch at the last second and if you fail, he gets hit before his fist connects with the boss' face.
Done in Yakuza 2, or Ryuga Gotoku 2. The final battle with Ryuji Ghoda, the final quick time event results in an epic cross counter! Almost as epic as the MGS4 one referenced above. Incidentally, Yakuza borrows heavily from MGS, among others, obviously including Ashita no Joh.
In the end of Viewtiful Joe 2, Joe and his father and Big Bad, Jet Black wound up in this. Jet then commented on his son's "Strong jaw".
Final Fantasy Tactics A2 has as a Master Monk ability named this: however, instead of either being a support or reaction ability that activates when the enemy character has a Counter as their reaction ability and reproducing the normally expected results, it's actually just an action ability that does more damage than normal (often double) and bypasses an enemy's counter, if the enemy has a Counter skill.
Bruce Irvin from Tekken can do a cross counter(called the Nightmare Punch) when the player times it with an opponent's punch. Also subverted in Tekken 6: Bloodline Rebellion's arcade intro - Both Jin and Kazuya evade each others' fists.
Someone made a nice long video of Bruce countering people all day. It looks like he can't double KO unless you do the punch too late, and if performed successfully, he never actually gets hit by the opponent's attack.
Heihachi also has a kick variation of this, performed against normal right kicks that hit high if you're hit during the active frame of the move. The difference with his version from normal Cross Counters is that while the attacks from both parties are generally simultaneous or near-simultaneous with them, Heihachi just takes the hit, and while the opponent just stands there dumbfounded with their leg in the air firmly against the side of his head, he just kicks them away with his right foot.
Yet another version of this could be Heihachi's Headbutt Carnival throw, which is functionally identical to his other, similliar throw in appearance, but characters who possess headbutt attacks of their own can avoid getting knocked down by it and counter-headbutt Heihachi right back...who can then counter-counter their headbutt and repeat the sequence until either character screws up the input or runs out of life first.
Paul Phoenix and Forrest Law perform a cross counter in their ending in Tekken Tag...but instead of a punch, they both kick...and instead of their faces, well, their reactions say it all.
In MadWorld with the power struggle between Jack and the Black Baron, trading a jab, an uppercut and a headbutt. If Jack wins, he ends with a hammer fist with both hands, while if the Black Baron wins, he lets loose a Single-Stroke Battle of Rapid-Fire Fisticuffs with explosive punches.
Persona 4 features this in Yosuke's Max Social Link event where Yosuke wishes to be seen as the Main Character's equal. In response, they choose to have a Ho Yay-filled brawl that ends with one of these.
In the climax of the Final Fantasy XI mission pack A Shantotto Ascension, after the final battle, the player is treated to a cutscene in which two giant Shantottos duke it out in Yhoator Jungle, ending with a spell powered cross counter. The fake falls while the real one stands tall. And this was not the actual characters fighting, but their spell powered avatars.
This is actually possible in the Super Smash Bros. games, though it all comes down to whoever's attack connected first.
Injustice: Gods Among Us has a variantion of this: When a counter is initiated, both characters are knocked back, recite character-specific lines and attack each other simultaneously. During the clash, players need to bet portions of their super meter to earn the upper hand. Whoever loses is knocked back and takes more damage. If it's a tie, then both characters are knocked back and take little damage.
In Transformers Prime, Optimus Prime and Megatron perform one during the opening theme, with the show's title appearing before the moment of impact. They do this to each other a few times in the actual series, as an Opening Shout-Out.