Oldboy (2003). On the very impressive one-take scene in the hall, the main character takes on countless mooks by himself aided only by a hammer. Sorta justified in that the main character spent over 10 years working out and practiced fighting, whereas the extent of practice the gangbangers he faced had was probably limited to intimidating people with weapons. And he didn't make it out unscathed.
Played with and lampshaded in Spy Kids, when two good guys are easily overpowered by two robots... then later in the film, four good guys come up with a plan under the assumption they can hold their own against 500 of those same robots. Luckily. Floop ends up reprogramming them to render them harmless just in time.
Gregorio: I'll take the hundred on the right… Ingrid, you take the hundred on the left. Carmen, hundred center-left. Juni, center-right. It'll work. It'll work.
Any time a group of ships appear, be it Klingon or Federation, count on them getting wrecked. A single ship, especially if it's named Enterprise, is going to kick ass. This is hilariously evident in the series even moreso (see TV examples). Of course, in the film, the one and only time that happened was when everyone was showing up without a clue that there was an enemy, and the same ship could have wrecked the single ship too at that time, even with warning.
Inverted in a deleted scene from the same movie; right after we see the Narada destroy the Kelvin, a large number of Klingon ships decloak and are able to capture it. (Granted, the ship had been somewhat damaged already.) Later, it's flipped again, Uhura picks up the Klingon transmission that a Romulan vessel wiped out over 40 Klingon ships during their escape.
Star Trek Into Darkness: Several squads of Klingons vs. four main characters. Three guesses who wins and the first two don't count.
Batman Begins skirts the edge of this trope. Bruce Wayne only fights one member of the League of Shadows during his escape (all the others were too busy dodging explosions); still, one might wonder how Bruce was the only ninja to escape the exploding dojo. (The answer: he wasn't). When he takes up the Batman mantle officially, he is able hold his own against four ninjas at once. This is Lampshaded to a certain degree with Batman's training as its designed to teaching him how to face vastly superior numbers and Ducard even declares Bruce his greatest student.
The Matrix trilogy: This applies to Agents and other superpowered avatars of computer programs in the Matrix throughout the trilogy. Mostly justified in that whenever someone's facing a large group of them, that someone is Neo after unlocking his powers as the One.
When Neo and the others face the Merovingian's henchmen, just two of them go after Morpheus and Trinity and give them a lot of trouble, while Neo handles the rest. In addition to Neo being Neo, this is caused by the fact that those two are Made of Air.
Seraph fights Neo alone and they seem evenly matched, with no particular explanation as to why Seraph would be so much more powerful than everyone else.
In Scott Pilgrim vs. The World Scott has little trouble mopping the floor with Lucas Lee's(The second evil ex's)stunt team, while only being able to defeat Lee by goading him into doing an insanely dangerous stunt on his skateboard.
Repeated just before the battle with Gideon. Scott effortlessly mops up mooks en masse before settling into a one-on-one Boss Fight that goes wrong.
The list just wouldn't be complete without robots. In I, Robot, Will Smith's character Spooner is able to survive and utterly destroy two massive truckloads worth of corrupted robots during the highway sequence, but the scene gets really serious when he realizes that there is one (albeit handicapped) robot leftover. Partially justified in that he defeats the two truckloads worth of robots with Car Fu and his gun and the single robot he faces unarmed.
There's a scene in the film where the older model NS4s try to protect Spooner from the new NS5s and just get the crap kicked out of them, regardless of number. They do manage to slow them down, though.
In The Princess Bride, Fezzik admits to falling prey to this trope when he starts having trouble fighting the Man in Black.
Fezzik: I just figured out why you would give me so much trouble. Man in Black: Why is that, do you think? Fezzik: Well, I haven't fought just one person for so long... I've been specializing in groups, fighting gangs for local charities... that kind of thing. Man in Black: Why should that make such a difference? Fezzik: You see, you use different moves when you're fighting half a dozen people than when you only have to worry about one.
The Jedi being overrun by Clone Troopers in Revenge of the Sith is another example of Jedi getting gunned down en masse, only for the named Jedi to easily survive and fight the troopers off.
Take the scene in Revenge of the Sith where Mace Windu and three other Jedi are attempting to arrest Palpatine. Palpatine instantly kills the first Jedi, then kills the second right after. The third Jedi survives for maybe five more seconds before also getting killed. Now that there is one more Jedi left, Mace manages to overpower Palpatine after a epic battle (though he may have let him). Mace Windu is, after all, Badass Incarnate.
There's also TIE Fighters, though this is more easily justified. The Expanded Universe explicitly references one of the common justifications on this page—that a large number of starfighters have to be more careful when fighting a smaller number of starfighters—and then justifies it further by Rebel X-wings having shields and TIEs not (which itself tends to lead to higher survivability for the Rebel pilots, who thereby learn from their mistakes).
Another Expanded Universe example: After the Brotherhood of Darkness imploded magnificently after Ruusan, Bane was left to rebuild the Sith. Instead of building a large army of Dark Side wielders, and dealing with the Chronic Backstabbing Disorder that came with it, he chose to take just one apprentice. Once the apprentice learned all they needed, they were to slay their master, take a new apprentice, and the cycle begins anew. Arguably, since the Sith lasted 1000 years under this idea, and it was the Sith dynasty that spawned Palpatine, it was the most successful. It's implied in the books that he got the idea from Revan's holocron. Not surprisingly, one of BioWare's writers was behind the Bane books.
"Only two shall there be, a master and an apprentice: one to embody power and the other to crave it."
The above could also be applied to the end of Return of the Jedi, wherein Luke is the last living user of the Light Side of The Force, thus the only person channeling its power in concentrate, enabling him to defeat two Sith whose purposes are divided (it helps that Darth Vader is having a Heroic BSOD of the Conflicting Loyalty variety).
In Kill Bill Volume 1, the Bride is able to slice through the numerous Crazy 88 members like butter with her superior katana, only having trouble when she faced the General and Gogo Yubari one-on-one. Of course, they weren't technically Crazy 88's but rather co-dragons but there's nothing to distinguish them from O-Ren's other Mooks aside from the fact that they had names and fought the Bride one-on-one.
In Starship Troopers the bugs are incredibly strong when there's just one or two of them in the screen, with close range and concentrated fire from multiple machinegun-equipped soldiers being required to kill them. When the troopers are defending the fortress, they can just spray down hordes of the same bugs with the same rifles that barely worked before.
In The One, it is quite literally a law of the multiverse that "power" is spread between the different incarnations of a person across universes, and criminal abuse of this has naturally ensued. The Big Bad and sort-of Evil Twin to the hero partakes in killing off their "other selves", such that by the final fight both are superhumanly capable.
In Raiders of the Lost Ark, Indy fairly easily takes out half a dozen Nazis on the truck transporting the Ark. But he nearly gets killed when there's just one Nazi left.
When Indy faces multiple mooks in Indiana Jones and the Temple of Doom, he knocks each of them out in quick succession, but when a single mook tries to garrote him earlier in the film, it leads to a not-so-quick struggle.
Equilibrium: In the final fight scenes, Preston is surrounded by six elite mooks and takes them down in about five seconds flat. There follows a duel with The Dragon ... well, kind of, since, in defiance of the trope, The Dragon, who fought Preston to a draw in a sparring match earlier in the movie, is taken down with three invisibly fast swipes, the last one of which ends with The Dragon's face getting sliced off. And then comes the Big Bad, who has more ninjutsu than any of his men combined, and who matches him gun for gun in the movie's final duel.
The trope is played straight in any of The Karate Kid movies whenever Mr Miyagi gets involved in a fight. Three, four guys, one big Caucasian guy ... doesn't matter. Old guy always wins.
Aragorn in The Lord of the Rings films faces dozens of orcs at a time throughout his adventures. The only time he seems to be having any difficulty is fighting one-on-one with the Uruk-hai leader and the troll.
A single troll was giving the entire group of heroes a hard fight in The Fellowship Of The Ring in a rare heroes vs. villain example.
When Optimus Prime fights Megatron in Mission City during Transformers, he gets his ass beat. When he fights the upgraded Megatron, Starscream and Grindor at the same time in a forest during Revenge of the Fallen, he holds up pretty well and even manages to kill Grindor, and take off Starscream's arm in the process. It's implied that Optimus held back in the first since there were bystanders, whereas he could cut loose in the sequel, proven in the forest battle where Optimus revealed he has two swords. In a real world justification, ILM wasn't too sure about the CG effects in the first film, so they kept the robots in the background. They went into the sequel knowing the CG was viable. Also, Optimus lost the second fight, fatally, when Megatron snuck up on him while he was finishing off Grindor.
Ash only fights one deadite at a time in the first two films. He ends up getting thrown into a lot of shelves when facing a single one. But once he has to fight a whole army of deadites in Army of Darkness, he conveniently gets a sword and starts slashing them up left and right.
He also took a serious level in badass near the end of Evil Dead 2. As can be seen in the theatrical ending to Army of Darkness, single deadites aren't much a problem for him anymore either.
In Dawn of the Dead (1978), Roger and Peter frequently punch out and knock back zombies with ease when facing them all at once. And then a lone zombie "disguised" as a mannequin catches Roger off guard and has to be dispatched without any ease at all.
In Face/Off it seems that all FBI agents, cops, security staff, and special agents are inept at facing off against Castor Troy. In just the opening shootout, Castor offs FBI agents single handedly with just two pistols (and at one point a shotgun he takes from a dead SWAT officer) until Sean Archer has a chance to face him one on one (for some reason the dozens of other agents stay out of the action - but then again, Archer's pursuit of Castor is more or less driven by personal issues). Castor reduces these agents to mere red shirts all throughout the film, when in reality said agents should be much better trained to have the upper hand in a gunfight. Not even the SWAT teams are immune as many of the agents shot dead during the shootout at Dietrich's loft are wearing paramilitary gear and submachine guns. Seriously, the Los Angeles FBI field office has to be running short of men to adequately staff it by the end of the movie.
In Pirates of the Caribbean: At World's End, toward the end when the pirates find themselves outnumbered and outgunned and standing off against the East India Company's hundreds strong fleet it turns out that the EIC only bothered to send one ship into combat — Davy Jones's ship. The rest stood back and didn't bother joining in the battle. Of course, it kinda makes sense to send an extremely powerful and essentially immortal ship to do battle with a single pirate ship, especially if you can take the other ships alive when they surrender. saves lives, saves money, and it's just good business.
Any Bruce Lee movie, where he's outnumbered 80:1; and when they use weapons, he whips out his nunchucks to do things the lazy way.
Ninja Assassin plays with this trope a bit. Raizo needs about 2 minutes work to down the lone ninja sent to kill Mika, but when faced with dozens later, he mows through them as though they were blades of grass.
13 Assassins both justifiably invokes and averts this trope. The thirteen are almost all skilled samurai, who have either participated in real duels and battles or have been trained by those who have, whereas 99% of the small army they must face have no real experience. The outcome - they kill everyone, but nearly all of the group dies.
In the Mega Man film, the Blue Bomber gets into a confrontation with all six robot masters at once before the individual fights begin. Fighting the whole gang is no problem, but alone we get real fights. Especially noteworthy is Elec Man who nearly kills Mega Man, until he gets saved by Blues/Proto Man.
The Alien franchise invokes this trope. The first movie has a single xenomorph terrorizing a ship of miners and the third has one xenomorph menacing a prison colony. The second movie and fourth movie have entire swarms of them that seem easier to kill. This is very easily justified by the fact that, logically for their respective settings, there was no effective weaponry present in the first and third films. Presumably, the lone creatures in the first and third films were every bit as vulnerable to gunfire, but that doesn't make a difference when there are no guns handy.
At various points in the Dollars Trilogy, Clint Eastwood effortlessly guns down three or more men with his trusty pistol. The only times where there is any doubt of him being successful is when he's only facing one or two opponents.
Happens in every Zatoichi film. The smaller the group is, the bigger threat they are. Also in the group of useless mooks, there is one skilled samurai/ronin, who is the biggest challenge and poses the greatest threat, though that is frequently inverted, sometimes the "Elite Mooks" go down as easily as the rest.
In a rare example of this trope being used against the good guys, the titular characters of "Ninja Cheerleaders" go through large groups of big mean men like it was clearance day at Macy's, but are completely overmatched by a single Dark Ninja during the climactic battle of the film.
You Only Live Twice. The massive army of ninja is slaughtered when it initially attacks Blofeld's lair. They become incredibly effective after Bond and Tiger Tanaka takes a hand and help out.
At the start of X-Men: Days of Future Past three Sentinels pretty much make a total party kill with one only losing an arm. For the finale even after bottle necking the ships with stormy weather and an exploding aircraft the remnant still destroy more Sentinels than at the start.
In The Chronicles of Riddick Toombs attempts to invoke this by going after Riddick with a four man crew, but Riddick takes a very dim view of this, and dispatches them easily.
"A four man crew for me? Fuckin' insulting."
He comes with more people next time. Just five. And Riddick allows himself to be captured.
In Teenage Mutant Ninja Turtles (2014), the four turtles and Splinter have no problem fighting off the numerous Foot soldiers but have significant trouble when it comes to fighting Shredder. Justified in that Shredder is far better trained and stronger than the average Foot soldier.
The assassins in Hero effortlessly carve through thousands of palace guards in order to reach their target, the Emperor, who by himself is much tougher than his men. This being a Wuxia film, this is hardly surprising, as the assassins' abilities are the very model of a Charles Atlas Superpower.
Captain America: The Winter Soldier has both titular characters mow down several mooks easily, and only have a truly difficult battle with each other. It's justified in that Cap and the Winter Soldier are the only enhanced beings in the entire movie — everyone else, while extensively trained in combat and dangerous in their own rights, are still baseline humans.