Given the Doctor's status to various people across the universe as basically a demigod, you can argue that a few people have done it to him too. Including Rory.
Xena: Warrior Princess: played fast and loose with this trope. For a time, Xena had the power to kill gods, and exercised this ability on most of the Olympian Pantheon.
Xena attempted to use this power on the archangel Michael, too.
Not to mention how often she beat the living crap out of Ares, the Greek God of War.
Or how she killed Callisto, while she was a goddess. And the Bacchae god Bacchus. And the war god Kal. All before ever gaining the ability to kill gods.
Or how she killed Mephistopheles. The King of Hell. As in Satan himself. Plus, not a full 72 hours afterward, Xena was singlehandedly responsible for making Lucifer the new king of hell.
Or how many times she put a stopper in the plans of Dahak, the ultimate evil god who was once described as 'The blind force behind every evil deed'. Though Xena never got the chance to fight Dahak herself, (something he should be incredibly thankful for) she was indirectly responsible for every defeat he ever suffered including his final defeat, and death, at the hands of Hercules and Iolaus after his introduction in 'The Deliverer', and for the deaths of both his daughter, the demigoddess Hope, and also his grandson, The Destroyer.
Or how, in the finale she killed Yodoshi, a poweful demon-lord, who had consumed both the souls of 40,000 people Xena killed by burning down the town of Higuchi, and the souls of anyone to die in all Japan since. After adding all of these souls to his power total, he was effectivley stronger, more deadly, and arguably more indebted to Xena than anybody she had ever come up against.
For one villain (the Judge), all the mystical texts declare that "no weapon forged" can stop him. However, as Xander realizes, those texts predate modern weapons. And thus, Buffy takes the Judge out with a rocket launcher.
Some of their Big Bads were essentially demon gods, who they eventually had to defeat to go on to the next season. By the end they faced against The First Evil.
Let's not forget Willow. She hurt the Egyptian God of Death when he refused to bring Tara back from the dead. She hurt a god!
Willow did this to Glory long before Osiris. Twice. Once in a Roaring Rampage of Revenge via lightning and a bag of knives (although all this really did was piss her off), and the second when she restores Tara's sanity, and blew Glory away like she was a piece of paper. Granted, Glory got back up seconds later, but seriously weakened. Justified in this case, the act of restoring Tara's sanity took energy out of Glory.
Buffy does the same thing later in the season, first with the Orb of Dagon, then with a hammer, then Xander does it with a wrecking ball.
Giles does so in an unusual way, by smothering Ben, the human holding cell for the Hell God Glory, thus, indirectly killing Glory. It's more astounding in retrospect than in the moment, but still.
The Scooby Gang has, several times, killed an Old One, the original, nearly all-powerful demons that originally inhabited Earth.
The first time was in mid-season three, in the episode "The Zeppo", when they killed the Hellmouth demon from the first season finale.
They did it again the season three finale. When the Mayor turns into an enormous demon after his Ascension, he's morphing into an Old One, which Buffy proceeds to kill with lots and lots of explosives.
Taken a step further in the Angel and Faith comics as part of Season 9. Angel and Faith go to Quor'toth, the dimension Connor was imprisoned in during season three of Angel. Once there, they inadvertently awaken Quor'toth, the extremely powerful Old One residing there. Willow then proceeds to fight it, one-on-one. And wins. Keep in mind, this was an Old One so bad that its dimension is called "the darkest of the dark worlds".
Buffy also took out the invincible Mayor and Caleb.
Literally occurs in Star Trek: Deep Space Nine, in which Q creates a boxing ring and begins taunting Sisko, and when Sisko has enough of it he flat out punches Q. Q remarks, "You hit me. Picard never hit me!"
Also, in the Grand Finale, Sisko takes out Gul Dukat after he's imbued with eldritch power as the emissary of the P'ah Wraiths with an extremely crude bull rush.
This is a recurring theme in Deep Space Nine, albeit mostly metaphorical. The Gods of the Dominion are the main antagonists for much of the show (although they are in fact changelings just like Odo.) And they stated that a type of radiation is harmless to humanoids but kills non-corporeal life forms, such as the Gods of Bajor in the wormhole and their Evil Counterpart, the Pah-Wraiths. You'd almost think they introduced religion into an entirely secular setting just to make this point.
It is an accepted part of Klingon culture that ancient Klingons found the gods to be troublesome, so they slew them. According to Klingon myth their Gods were destroyed by the beating of the hearts of the first two Klingons and set the heavens on fire.
In Star Trek: Borg, a Full Motion Video game where Q assists the player in taking revenge against the Borg, the player is given the option to either punch Q in the face or deliver a Groin Attack to him.
This may or may not be a Call Back to the episode Future Echoes way back in Season 1 when Rimmer tells Lister "[He] can't whack Death on the head", to which Lister responds, "If he comes near me, I'm gonna rip his nipples off!"
Happens damn near literally in Farscape — the invincible space vampire Maldis is defeated in his second appearance with a couple punches and gunshots.
In Torchwood, Owen beats Death in a wrestling match.
Technically, he just held Death until it died of starvation for lack of souls to consume, as at this point Owen himself is technically dead.
Let's not forget the time that Captain Jack Harkness kills Abaddon by having him absorb Jack's immortal life force until he overdosed (or something).
In the season 5 finale of LOST, Benjamin Linus kills Jacob. Yes, that Jacob; the guy who's pretty much been played as God since his offscreen introduction to the series.
A milder version in the next season when quasi-immortal Richard, the one character whe never suffered an injury, gets knocked out and carried away. Not as big a deal when you realize the guy knocking him out was the series's real Cthulhu...
Subverted a few episodes later, again with Richard. Much like Ben, Richard is talked into killing Jacob. Unlike Ben, he gets his ass kicked. Clearly Jacob got lazier over the years, or tired of the job.
Another mild version occurs in "The Candidate", Jack and the Man in Black/Flocke are running towards the submarine while Flocke is (unknowingly) saying that Locke was wrong about Jack needing to stay on the Island. Jack reveals this and then uses his gun to knock Flocke into the water. For a being who had wiped out countless people without suffering a scratch, this was quite the humiliating moment.
An even better example, in the Series Finale Jack leaps off of a cliff in the middle of the rainstorm from what seems to be 10 feet and bashing The Man In Locke with a earth shaking right hook. And, credit where credit is due, Kate saved him a bullet.
What about when Eko stares down the Smoke Monster? Yes, not quite punching out, but back then, when Smokey was the pilot-mutilating, howling-in-the-jungle, enigmatic death machine, just seeing him and surviving was pretty lucky.
The made-for-TV movie Fallen on ABC Family, where the hero is the Antichrist, and he exists to redeem his father Satan, but instead, he kills him.
In Mighty Morphin' Power Rangers, Rita Repulsa summons this ancient spirit Lokar (in the original Japanese series Kyoryu Sentai Zyuranger, Lokar's name was "Dai Satan." Yeah). The Power Rangers defeat Lokar and send him running, screaming in pain. That's right. The Power Rangers beat the devil in a fight. In their first year (!).
Season one also had a normal-sized Green Ranger take on Megazord, who is a talking creature called the Great Beast God in the source material. His lasers are no match for the mastodon shield, and later he sort of cheats by kicking the team out of the cockpit, but he still gets points for trying.
In season three, Rita's father Master Vile arrives. Vile is described as the most evil being in the Universe. The Power Rangers deliver such a beatdown that Master Vile runs back to his home planet within about five episodes.
In season eight, the Lightspeed Rangers' major arch-enemy is a demonic elder being named Queen Bansheera. Bansheera's ultimate plan is to open the gates to monster hell, and have demon spirits lay waste to planet Earth. Carter, the Red Ranger, manages to defeat Bansheera in hand-to-hand combat, then drops her into monster hell, and seals her in.
Admittedly, Carter DID have a bit of help as the other 5 Rangers were trying to pull him OUT of the portal to hell whilst Bansherra was pulling him IN, until Diabolico got her to let go and pulled her in whilst Carter was pulled out and the portal sealed.
In season ten, the Wild Force Rangers spend the season up against Master Org. In the finale, when Master Org gains an upgrade, he manages to kill a god, the deity Animus. But through the strength of the Rangers' belief, they summon one hundred zords who focus their ultimate attack on Master Org and turn him to dust.
In season thirteen, the final villain that the Power Rangers Space Patrol Delta face is a giant sentient space-ship named Omni (who had been forcing the other villains to rebuild him all season-long). The SPD Rangers bust out their respective zords (including a sky-scraper that gets up and walks around), and you can guess what happens.
In season fourteen, the final villain for the Mystic Force Rangers is a Cthulhu-esque demonic entity named the Master, who eats magic. After murdering the Rangers' family and mentors, he consumes their magic. But the belief in the Rangers (from the town they had spent the year protecting) restored their powers (and their dead mentors). The Master exclaimed, "Give me that magic!" The Rangers oblige, channeling their powers into a limitless blast of energy, that they force down the Master's throat until he explodes.
In season fifteen, although it was done very badly, and was absolutely anti-climactic, the villain Flurious donned the Crown of the Gods in the season finale, brought down a glacier on the Rangers' hometown, but the Operation Overdrive Rangers manage to kill him.
In season fifteen's yearly team-up episodes, a particularly vicious and powerful giant monster is thrashing the team's zords. Mack, the current Red Ranger (although at the time, he'd resigned) runs towards the monster holding the magical sword Excelsior, and manages to kill the 30-storey-tall monster, using nothing but the sword. Only four Rangers in the entire history of the show have ever managed to defeat a giant monster without using their zords (TJ the Red Turbo Ranger, Eric the Quantum Ranger, and Tommy as the Black Brachio Ranger being the other three). But Mack is the only Ranger to ever destroy a giant monster without even morphing.
In season sixteen, the Power Rangers Jungle Fury team spend the season fighting Dai Shi, an ancient elder-being. Once Dai Shi manifests physically, the Rangers team up with Dai Shi's pawns (Jarrod and Camille), and Jarrod lets himself be consumed by Dai Shi to destroy the entity from the inside out. Jarrod survives. Dai Shi doesn't.
The Samurai Rangers continue the trend, with their final battle against the demon overlord Master Xandred. They've tried to seal him back inside the Underworld (which failed), they tried to exploit a weakness (which failed), they used a special one-of-a-kind weapon to hurt him (which failed). Growing increasingly desperate, their plan eventually just becomes, 'hit him until he drops'. It works. Twice.
In the first few seasons of Stargate SG-1, the eponymous group is the main thorn in the side of the Goa'uld Empire, who fancy themselves gods. The Goa'uld are beaten soundly at the end of the second part of "Reckoning", though they manage to survive but are currently warring amongst themselves. Then there are the Ori in the last two seasons, who are the closest thing to godly that the series can get. They're all killed by a MacGuffin, but their physical embodiment Adria gains all of their power. She, however, is apparently occupied in an unending battle with Morgan Le Fay.
Don't forget Sam Winchester in Supernatural, granted he was drugged up on demon blood at the time but he kicked the horseman of famine's ass (in a Ghost Rider-like method). There's also his killing of Alastair and wrestling control of his own body from Satan, before throwing both of them into Hell.
Or Dean Winchester, who has taken out at least 5 supernatural beings ( Azazel, the Whore of Babylon, Zachariah, Eve, and Dick Roman) that he had no business defeating or even approaching. With nothing more than a GED and a can-do attitude.
The finale of Ashes to Ashes, in which - among other things - Gene Hunt PUNCHES SATAN IN THE FACE. No, seriously. Jim Keats isSatan.
In Kamen Rider Double, the Utopia Dopant isn't a God but is pretty close to Omnipotent. In the end, Double beats the stuffing out of him. Though in his defense, he was just caught in his evil lair blowing up around him and they turned his strongest ability to overload him, still, up until then, he was he steamrolled everyone in his path.
In Ultraman Tiga, the final monster was Ghatanothoa, the first born of Cthulhu, who covered the entire planet Earth in darkness. When Tiga fought this Great Old One for the first time, he got turned into stone. But after being revived by the light of humanity (the episode was named "To the Shining Ones" where children who are still believe in Ultraman Tiga (most adults, save the defence team, lost confidence) turned into light and merged with Tiga), Ultraman Tiga punched and sent it flying, kicked it, used signature beam attack on it, and finally killed it with a new beam attack, restoring Earth from its darkness.
Babylon 5 is one big epic about punching out Cthulhu. It ends with the remaining Cthulhus just deciding to leave, only for the viewers to be treated to the Thirdspace Aliens who are as close to Cthulhu as the other First Ones are: they're immeasurably OLDER than even the Vorlons and Shadows, they live in a dark dimension, they have immense telepathic powers surpassing even the Vorlons, AND a (presumed) member of this race which tried to kill Sheridan looked like a squid/octupos. Series creator Staczynski has also said that the Thirdspace aliens were based on the Cthulhu mythos.
Of particular note is Londo Mollari, who first asks the Shadows to depart Centauri Prime peacefully. When they refuse, he destroys the entire island they are based on with nuclear warheads he had secretly planted there beforehand.
Played for laughs in the Argentine comedy Casados Con Hijos. Pepe Argento is visited by Death, who wants to take him. First, they try to settle things playing Truco (an argentine card game), and get to a tie. Then, they improvise a net and decide things by soccer penalty kicks. Death is about to win... and then Coki gets into the house, confuses Death with a common burglar, and attacks him. He missed the penalty kick, so he lost.
Once Upon a Time: Hook shoots the dark one's girlfriend, and causes her to lose any memory she had of said dark one. Emma sums it up nicely to Hook handcuffed to his hospital bed:
Emma: You're chained down. He's on his feet, immortal, has magic, and you hurt his girl. If I were to pick dead guy of the year, I'd pick you.