Team Rocket, the Trope Namer from Pokémon, beat the crap out of Ash's Pokémon when they were allowed to run Viridian City's Gym using Giovanni's Pokémon, at least until Ash managed to regain momentum and beat them at their own game. There have been a few other instances where Team Rocket has been successful in battle, but it was because they were trying to do something good for a change. Their victories never lasted too long, and they were often sent flying at the end of the episode anyway.
Jessie (while under her Jessilina alias) has actually become competent enough to win Pokémon Contests all on her own without cheating (though she has considered it at times.) She lost out on winning her fifth ribbon needed to get into the Grand Festival, but Dawn (or rather, a Dawn lookalike by the name of Princess Salvia, long story) gave her the sixth ribbon she had just won. Jessie gratefully accepted it and made her way to the semi-finals against Dawn in the Grand Festival.
In Off the Unbeaten Path, James won a contest that involved teamwork with one's own Pokémon. He used Mime Jr. and was steadfast in playing by the rules despite Jessie's repeated attempts to encourage him to cheat. So this goes with the "Team Rocket can win if they act like good guys" rule.
Nearly happened when James turned out to be an expert at a sport that used flying Pokémon. Once again, he refused to cheat, and he lost by only the tiniest margin.
Meowth, who is usually a pitiful battler, once defeated a rival Persian in a one swipe knockout. He also managed to defeat Brock's Onix in a tournament for ownership of Togepi (albeit by throwing water on it first).
Interestingly, repeated encounters with Ash and friends has been like Training from Hell to the team, giving them superhuman damage resistance, among other things. Meowth himself commented that a powerful electric cage was nothing compared to Pikachu's electric attacks. They also learn from their mistakes, though in the process, usually make new ones. An example would be Charmander's debut episode all the way back at the very start of the original series; they use rubber coated equipment to nullify Pikachu's electric attacks, but didn't bring any fireproof equipment.
Heck, in some later episodes, Team Rocket actually does some heavy damage to other trainers. In general, Team Rocket manages to win when the plot requires it - Jessie fighting her way to the end of the Princess Festival tournament, Jessie and James defeating the Eevee Brothers, etc.
This occurs even in early episodes— in "The Punchy Pokémon", various trainers are participating in a Fighting-type only tournament. Though Ash beats them in the end, the trio very successfully steals a Hitmonlee and thrashes their competition with it through a combination of regular battling and standard cheating. This is pretty notable, since they beat a Hitmonchan raised by a trainer who LEFT HIS FAMILY to train it.
In The Thief That Keeps on Thieving! they actually managed to catch the wild Pokémon that the character of the day was after and send it to their boss. Of course, he sends it back to them and it promptly evolves, giving Jessie a new Yanmega. Said Yanmega then proceeds to get as close as any Team Rocket Pokémon has to blasting off Ash & co.
They seem fairly competent whenever they are not dealing with Ash and co. - remember that they had wanted posters with their first appearance? - and many of their plans worked… until Ash got involved. According to Pokémon Chronicles, Jessie and James weren't just competent, they were THE BEST operatives in Team Rocket history! In fact, in their first appearance they managed to not only steal ALL the Pokémon in the center (owned by full fledged trainers) and wreck the place, BUT would have gotten away scot-free if not for Ash using a team of Pikachu to supercharge his own! Then... they stopped doing real evil in favor of following Ash around and trying to steal some noob's yellow rat.
In the Best Wishes! series, they got new uniforms because of a PROMOTION.
Even wilder, they became competent and so far have stayed that way. They almost capture Pikachu and Iris's Axew. Key and operative word: almost. We're 40 episodes in and they've yet to blast off once (the blasting off role was taken by a Sandile who appeared in a couple of episodes). They generally stay away from Ash and company, however, because of their new mission.
It's possible they'll be competent all through the Best Wishes! series, because they're supposed to be the spark for Team Plasma's appearance.
So far this season, Giovanni has given them one mission. The goal of said mission was to collect dream energy from an abandoned research facility in order to help with Team Rocket's plans to conquer the world. While they failed to capture the Pokémon of the day, the episode where they put this plan into action basically ended with Giovanni congratulating them on succeeding and telling them that he had people looking at the energy to see what they can do with it. That's right, Team Rocket just successfully completed the first step in a plan for world domination.
And now they've managed to break into a top-secret research facility and steal data on a meteorite that gives off some kind of ultra-powerful energy that can be used for World Domination.
A great example of this occurs in the Kami trio two parters. In the first, they set in motion the appearance of two of the legendary Pokemon, and then wait for Ash, since they know that he'll show up. Then they use him and his friends to summon Landorus. They are Genre Savvy enough to use the fact that Ash attracts legendary Pokemon to their own advantage. In the second, they locate an undersea ruin and are able to help Giovanni capture Ash, the gang, and Meloetta, who is the key to summoning the Kami trio again. They came close to taking over the Unova region, but Giovanni got possessed by the reflecting mirror used to transform the Kamis into Therian Forme, and Team Rocket had to actually help the twerps break the possession before Giovanni destroyed, rather than took over, the world.
A borderline example. In Otasukeman, one of the series from the Time Bokan meta-series, at the end of every episode the chief of the Time Patrol asked the two main groups of the Patrol to pick a choice between two special kinds of training. One group (who really were the heroes of the series, the titular Otasukeman, and always won the battles) always picked the pleasant, relaxing activity, when the other one (who really were the Terrible Trio, the "evil" Ojamaman, and always lost against the Otasukeman) always picked the nasty, gruesome Training from Hell. In one episode, however, the Terrible Trio chose wisely and won a nice boat trip over a calm river, while the heroes found themselves in a Japanese cemetery filled with angry ghosts.
Sonic X had this happen once, but not when facing Sonic. Usually Eggman's schemes fail miserably, and his machines and robots are useless, but then he goes up against some Metarex that are attempting to hurt Sonic. Without warning, Boko and Deko, his worst robots, become super strong and beat everyone down, and Bokkun delivers a powerful uppercut kick, clearing a pathway for them all. On several occasions, while never outright defeating Sonic, Eggman managed to distract or overpower him long enough to get away with a Chaos Emerald. He actually gets his hands on all seven at least twice over (though on both occasions uses them on a haphazardous death machine).
At the end of the first arc of Digimon Xros Wars, Bagramon easily takes all the Code Crowns and reconfigures the Digital World. Taiki, Akari, Zenjirou, and Shoutmon are blown back to Earth. While they're gone, Kiriha and Nene are forced into hiding, Xros Heart is captured, and the Digital World comes under worse oppression than before.
Florsheim once brought a werewolf to do battle against Astro Fighter Sunred… On an overcast night. After spending several hours waiting for the beast to transform, Sunred had had enough and went home. Vamp wonders if they can call this a 'win' until one of his combat goons tells him they probably can't.
Anytime The Shocker does anything right, it counts as this. But what stands out in particular was his appearance in the Ultimate Spider-Man book, where after countless, effortless losses to Spidey (who slammed the point home by cracking jokes), he managed to knock him unconscious. He then tied him up with chains, ranting and torturing him, and likely would have killed him if not for Kitty Pride and the NYPD finding his location.
In The Powerpuff Girls story "Smart And Smarter" (Cartoon Network Block Party #59), Mojo Jojo outwits Blossom, with her sisters' blessings! Blossom (who let her ego swell after being admitted to a special school) blows her ice breath which Mojo counters with a heat shield. The trail of melted ice reaches Blossom's foot (which she doesn't see) and she emits static electricity from her hands which in turn fries her to a frazzle. The ending panel has Buttercup shaking hands with Mojo.
Magical Troubleshoting Fighting Federation, a tournament with a crossover cast of various anime series, actually has Team Rocket win at least once, much to their own shock.
Hell, after a while they were the most popular team in the organization! And did a Heel-Face Turn because of it! And became one of the most successful teams in the crossover!
It's a series inspired by pro wrestling, of course the team with the most showmanship is going to win!
The second season's arc of La Serie De Ken is kicked precisely because of this, Team Rocket manages to steal all but one of Ken's Pokémon and he has to start anew with a new set to try to recover them, it also marks the start of the villains as Not-So-Harmless Villain and the series' Cerebus Syndrome.
A Powerpuff Girls picture strip story, "Diet With Honor," had Mojo Jojo making good on a threat to give Blossom "the spanking you so richly deserve."
In Cars, when Lightning brakes hard at the finish line, reverses, and pushes "The King" across. This time, however, when Hicks wins, he's the only one celebrating and is shocked when everyone starts booing him. Since he cheated by (intentionally?) wrecking "The King" in the first place, he had no business being shocked.
Megamind's plot starts rolling because of this, which is lampshaded by both Megamind's sidekick early on and Metro Man much later.
Zig-zagged with Wreck-It Ralph. The title character, a figure in a 30-year-old video game is tired of being the "bad guy" and schemes to get a medal to prove he can be a good guy. After accidentally landing in another game, "Sugar Rush," he helps an outcast little girl, Vanellope Von Schweetz, win a race, but he has to deal with the game's evil boss and a swarm of cy-bugs which were brought in from another game to this one.
Films — Live-Action
In The Great Race, the main character Leslie stops just short of the finish line and lets the Harmless Villain team win to show The Chick that he loves her enough to give up the race. Professor Fate becomes livid about this, and challenges Leslie to another race.
Presuming that the condition for villain victory is "kill the slayer", Buffy the Vampire Slayer has numerous examples: Spike legitimately out-fights and kills two Slayers, Drusilla effortlessly takes out Kendra the Vampire Slayer, The Master kills Buffy on two occasions (one time she is revived and the other in an alternate universe), and a random vampire nearly kills Buffy in "Fool for Love", and it's Riley that ultimately puts him down.
Even Harmony (probably the biggest joke on the show) managed to kill a Slayer in the episode "Harmonic Divergence" (although it was at least partially by accident) and she had a more earned victory in "Harm's Way" against another vampire (that one was technically a case of Evil Versus Evil, but she was clearly the lesser evil.)
If you count characters who nearly pull off kills until somebody saves them at the last second, then that opens up a much larger group, including the Gentlemen, Warren, Dark Willow, and Caleb.
Glory kicked Buffy's ass all over season five. Willow was the only one who managed to do any true damage to her. Well, her and Giles, but that was only because he killed her human host while she was essentially unconscious.
In Mighty Morphin' Power Rangers, Zedd and Rita would pull this off at least once a season. This usually involved the zords being destroyed and re-formed, and as such, usually happened when they had run out of Sentai footage and/or just in time for an action-figure shopping season. Topped by the series finale of Mighty Morphin, as the two actually do succeed in not only leaving the Rangers powerless, but also destroying the Command Center. Damn.
And in Power Rangers Lost Galaxy, Psycho Pink manages to actually kill a Power Ranger. She stabs a morpher with the Savage Sword, which created a massive vortex that threatened to destroy Terra Venture. The only way to stop it was Kendrix crawling inside and hitting it with the Quasar Sabre which killed her. Of course Psycho Pink is quickly defeated by the other rangers in their Megazord.
Doctor Who had the episode "Victory of the Daleks", which was exactly what it said on the tin; that is to say that the Daleks managed to accomplish their main goal and escape to tell the tale.
Star Trek: The Next Generation had the episode "Data's Day", where the Romulans managed to win one of the series' tense Neutral Zone stand-offs, recovering their spy and forcing the Enterprise to retreat. This is lampshaded by Commander Riker who notes "Some days, you get the bear; some days the bear gets you."
The Charmed ones don't always get away without a scratch. The list is actually quite long:
Inspector Rodriguez comes very close in the season 1 finale which has a time loop. Phoebe is killed in the first loop and Piper as well in the second. The only thing that helps the sisters is that Phoebe gets strong deja vu vibes whenever time resets.
Ginny in "I Dream of Phoebe" wishes the sisters dead. Of course they're still around as ghosts to ensure they don't stay that way. One of them possesses Ginny and tricks her into wishing them alive again (Aladdin rules don't apply here).
When Prue is turned into a teenager without her powers, she falls victim to a Dragon Demon and again has to be wished alive by a genie.
Phoebe and Paige are killed during a fight with Billie and Christy when the powers being used causes the manor to explode. Time Travel and Billie's projection power come in handy to ensure that it doesn't stay that way.
Phoebe and Paige are killed again in "A Witch In Time" when a warlock is able to strip them of their powers and incinerates them. Piper only narrowly escapes when Leo intervenes.
Quite possibly the most successful of all. The upper level demon Shax managed to kill Prue at the end of season 3. For good. In the same episode, Piper was also shot dead by a simple human.
Happens yet again with Axel in Disgaea 4. And when he wins this time, he really wins.
In Final Fantasy VI, Kefka's triumph in Thamasa is a complete surprise to the player. After all, almost every other encounter has consisted of Kefka casting a weak spell and then running away, and when Kefka seems to finally be serious in Narshe, he is still quite beatable. So when he appears in Thamasa, destroying Espers left and right, there is really no precedent. And right after that, Kefka destroys the world.
Touhou has this in the handful of games that you can actually play as Cirno. Or, you know, if you lose to Cirno in the regular games. Cirno's plotlines generally have nothing to do with anything actually going on, and involve her just trying to prove she's "the strongest".
In Great Fairy Wars, Cirno is the main character. While she mostly spends the game fighting her fellow fairies (hence the name), the EX stage boss is Marisa. Since canonically the main character(s) always win...
In Street Fighter II, once you can play as M. Bison, this trope can apply. If you win as Bison, his armies take over the world.
In the Dreamcast and PS2Wacky Races game, the final unlock is the ability to play as Dick Dastardly. It's worth going through all the trouble to do so just to win a race as him and hear the announcer's bewildered or disgusted reaction.
Team Skull from Pokémon Mystery Dungeon: Explorers of Time/Darkness/Sky was introduced as an easy first boss. In a later mission where your team is sent out to get Perfect Apples however, Team Skull brings their leader along to defeat your team, and then they take the apples you were supposed to find.
In Paper Mario Bowser once again starts the game's story by invading Princess Peach's castle. Peach sends Mario on him, predicting the usual result. Then Bowser pulls out the newly stolen Star Rod, boosting his strength, cue a Hopeless Boss Fight where your only choice is to let Bowser chalk up his first canonical victory against the plumber. Peach and even Bowser himself are completely astonished.
Playing E-102 Gamma's story in Sonic Adventure allows you to battle and win against Sonic in a brief mini boss. Amy stops him just short of finishing the job however.
In the Crash BandicootParty GameCrash Bash it is possible to win Adventure Mode as Dr. Cortex or one of his cronies, giving a bad ending where Uka Uka gains ownership of all of the crystals "and all of the POWER!!!". This is done in a more direct sense if you play the Adventure Mode in two player co operative with a good and evil player, allowing access to a hidden deathmatch where the two of you fight to determine the ending, thus get the extra reward of kicking Crash or Coco's ass as one of the Rogues Gallery before taking over the world.
Since they're playable characters, it's possible in the Ranma ½ video games for even complete scrubs like the Card King to kick everyone's ass and, at least in theory, get what they've been after all this time. Since the source material is a Sadist Show, of course, it never really works out — with the exception of Herb, who successfully conquers the world.
The page picture comes from Plague's Misadventures, one of the hosted comics in Bob and George. Sigma, who in this series is pretty much a nuisance Harmless Villain, actually succeeds in bringing down the space colony and bringing about the end of the world when the heroes shoot it down with the giant canon.
The Dimension of Pain demons from Sluggy Freelance, from their inception, had been largely Harmless Villains. When Torg wound up in their dimension, he easily withstood their attempts at torture, outwitted them, and escaped. After that they repeatedly tried to recapture him every year, but they could only send one demon at a time, only on Halloween night, and it could only stay until sunrise, and they inevitably failed in humiliating ways, to the point where Torg threw Halloween parties with the demons advertised as the main attraction. Throw in their wacky antics during the "Meanwhile In The Dimension of Pain ..." strips, and no one really took them seriously. Then "That Which Redeems" came along, and with the demons finding a way to bypass their previous limitations, suddenly they're conquering entire countries, butchering helpless bystanders, and outnumbering Torg 1000 to 1. Not to mention killing off Alt-Zoe.
The episode "Meet the Beat Alls" had Mojo Jojo, Princess, Fuzzy and Him team up into an ultra successful band, the "Beat All's", which the Girls were powerless to beat conventionally. Enter Moko Jono. True, Him is hardly a Harmless Villain, but Fuzzy, Princess and Mojo (at times) are pretty low on the threat scale.
In "Mr. Mojo's Rising", Mojo acquired the Girls' abilities and defeated them, only to launch into a navel-gazing session so severe that he didn't notice the Girls recover and turn him back to normal.
The episode "You Snooze You Lose" even had The Amoeba Boys on the verge of victory, albeit completely by accident, obliviously setting the Girls into a trap they stole from Mojo Jojo (until Mojo himself stopped the trap).
In "Him Diddle Riddle", Him challenged the girls to solve a series of riddles on time to find Professor Utonium or the professor would have to "pay". They found the Professor a few seconds too late and Professor Utonium had to pay... the diner bill. It was just a diner bill but, the villain won and the narrator didn't have anything to say when he'd usually say the day had been saved. It turns out to be a tainted victory however when Professor Utonium vows to never come to his diner again.
The episode "Moral Decay" has one concerning almost every single villain in the series. After Buttercup gets greedy when she realizes she can get money from the Tooth Fairy, she starts collecting villains' teeth from fights. She soon resorts to randomly beating them unprovoked. The other girls find out and organize a surprise attack on her, where the Rogues Gallery literally kick her teeth in.
The Grand Finale, "See Me, Feel Me, Gnomey" began with the city besieged by the girls' Rogues Gallery, and the girls getting their butts kicked to set up the main plot.
In one episode, the "superheroes" lost control of their powers and were badly injured, and Mermaid Man was too weak to fight. However, Barnacle Boy (who just had a Face-Heel Turn and called himself "Barnacle Man") decides to simply go back to being good, just because he can now have an adult-sized Krabby Patty. The other villains are later seen in jail, participating in the Everybody Laughs Ending.
In "Wishing You Well" he also gets his wish of growing to several hundred feet to "crush his enemies". His appearance ends with him happily knocking down random buildings in Bikini Bottom.
Designated villains The Really Rottens actually won in at two episodes of the Laff-a-Lympics. Usually most of their points were ruled invalid by the judges, but yep, a couple of times, the rotten bastards won. Note that the one time they won legitimately, they didn't like it at all. Apparently it's not a victory for then unless they won by cheating. An issue of the Comicbook Adaptation (Marvel #5) had the Rottens apparently renouncing their cheating ways and winding up winning. However, they were disqualified because The Great Fondoo and Magic Rabbit, who were "kicked off" the team, kidnapped Boo Boo Bear and Blue Falcon, took their physical forms through Fondoo's magic, and caused the Yogis and Scoobys to lose on purpose.
On a similar subject, one episode of Wacky Races actually ends with Dick Dastardly placing in first. But unlike the Really Rottens' example, he doesn't get to keep his victory, because the announcer then shows a slow-motion replay of the race's finish that shows that the Mean Machine stretched its front forward to give the illusion that he came in first (despite the fact that if you look at the actual finish, you don't see such a thing happening). Watch the clip here.
Dastardly actually won two races outright in the comic books: "The Scavenger Scramble" (Gold Key #7) and "Trek To Tazmania" (Archie Comics #1). There were catches to the victories, however. Hanna-Barbera Fun-In (Gold Key #5) had a one-pager of Dastardly pushing the Mean Machine across the finish line after Muttley bails on him, and he uses the trophy, filled with hot water, to soak his feet.
In an episode of Xiaolin Showdown in which Omi freezes himself so he can find his future self (doesn't work of course because he wasn't there) he ends up in a Bad Future where Jack Spicer has taken over the world. The crazy part is that he apparently defeated and captured the other three villains, despite them being far more evil and powerful.
On a lighter note, he also won in two episodes, one where the robot he sent lost the showdown, but he stole all the monk's Sheng Gong Wu (in the "shake the heroes out of their comfort zone" model), and another where Omi actually loses due to misusing a shen gong wu, and the episode has a downer ending. Despite being an Ineffectual Sympathetic Villain, hes had several Near Villain Victories as well.
Wile E. Coyote:(Holds up a sign) Okay, wise guys, you always wanted me to catch him. Now what do I do?
Also, in Cartoon Network's I Shouldnt Be Aliveshort on the Coyote, after spending almost a whole year attempting to attack and capture the Road Runner, he finally has him within his grasp (he simply laid out some bird seed and leapt at him while he was eating), only to discover that his finger muscles were too weak to do anything to him.
A bumper on The Road Runner Show (CBS, 1966-68; ABC, 1971-72) had the coyote diverting the Road Runner's attention by drawing a portrait of the two, the coyote in the drawing with a rifle in hand. The coyote grabs the Road Runner's neck only to have the coyote drawing blast him in the ass with the rifle.
In the original nine-minute long version of Duck Dodgers and The Return of the 24th and a Half Century Marvin the Martian seemingly achieves his goal of detonating the earth. With Dodgers distracted from his duties and earth's destruction almost certain, Marvin is left with no choice but to ensure the viewers "it's only a cartoon". Oddly this was cut from the shortened theatrical version of the short, though since it ends with Dodgers still having not stopped Marvin, the implication is still there.
In the Chaos Emerald four parter, Robotnik manages to outsmart or overpower Sonic on four consecutive occasions to claim all four Chaos Emeralds and transform into the "Supreme High Robotnik, MASTER OF THE UNIVERSE!" He handily defeats Sonic in their first bout, after which the heroes rely on a Temporal Paradox to defeat him.
The Super Mario World episode has Bowser actually make off with the money he made selling his mutant food to the cavepeople (or at least two bags of it), with Mario and Peach making no effort to stop him (not that they ever tried before, though). Perhaps it has something to do with the fact that his restaurant actually was a legal business, even though he was using it to turn the cavepeople into his Mooks.
He also kept the money when he sold televisions to the cavepeople. In the cartoons, someone cut Bowser a check and he's been abusing it ever since.
The Adventures of Super Mario Bros. 3 episode "Crimes R Us:" In spite of their massive failure to rob the Mushroom Kingdom Treasury, Koopa and the Koopa Kids do manage to get away with over 1,000 items stolen from the Mushroom citizens.
In The Super Mario Bros. Super Show episode "Flatbush Koopa," Bowser is attacking Brooklyn, and Mario succeeds in trapping him back in the Mushroom Kingdom. Only he realizes too late that he's trapped there too, and the episode ends with Bowser blasting away at Mario and the gang, who are running away.
In an episode of Justice League, a group of Superman villains teamed up, planning to use their combined talents to finally kill the big blue alien once and for all. Naturally, the Justice League wipe the floor with them before Superman even gets there, but they still manage to pull it off! The one who made the killing blow? ..... Toyman. Yeah, it was Toyman in a Humongous Mecha and Superman was really only sent thousands of years into the future and returned home at the end of the episode, but still. Toyman.
Possibly the only Tom and Jerry cartoon where Tom doesn't get utterly humiliated at the end by Jerry, Southbound Duckling ends with Tom... well, just watch for yourselves.
Tom wins in a total of 13 different cartoons including Million Dollar Cat, The Vanishing Duck and Duel Personality.
He continues this tendency in Tom and Jerry Tales, where at least half a dozen episodes end on him getting the last laugh on Jerry.
This pattern was replicated with Hanna Barbara's later cat and mouse team Pixie And Dixie and Mr Jinx in The Huckleberry Hound Show. Perhaps due to his even more ineffectual qualities, Jinx actually come out on top a fair bit more often than Tom.
Invader Zim has nearly succeeded in taking over the world/defeating Dib several times, only to be beaten by one Deus ex Machina or another. However, there is one time he did win: in "Bad, Bad, Rubber Piggies", he uses a time machine to repeatedly cripple Dib in the past until he dies in the present. To repeat - Dib, the only person standing in the way of Zim's plans of World Domination, is dead. Of course, then the Butterfly of Doom kicks in, and Zim is forced to hit the Reset Button, returning Dib to normal. Which really wasn't a win; Dib only died for a split second, and once he came back he was actually a greater threat than ever, almost killing Zim before he quickly hit the Reset Button. Neither Zim nor Dib ever gets a complete win, of course, but Zim does better than Dib fairly often.
In one episode Candace actually does succeed in busting her brothers. However, this turned out to be All Just a Dream.
We get a twofer when a time travel episode had her future self come back and bust them, causing a bad future where Dr. Doofenshmirtz rules. Of course, it gets fixed.
Candace also succeeds in busting the boys in "She's the Mayor" where it goes so far as Mom actually berates them. Unfortunately for Candace, time rewinds at that point.
Transformers Cybertron episode 25, "Retreat": Starscream pulls a Determinator on the Autobots, managing to steal the Omega Lock and the three Cyber Planet Keys found thus far. This after successfully betraying Megatron. He goes on to supersize himself and become a major threat on his own until towards the end, and his showdown with Galvatron.
Defied in ReBoot. In season 3, Hack and Slash would have succeeded in executing Cyris, but Slash refused to go through with it. It turns out Slash never wanted to win in the first place, counting on (now-absent) Bob to prevent him and Hack from doing anything too bad.
There is also 'Megabyte's Bane' at the end of season three. To quote:
Megabyte: No, you remember boy! How I turned defeat into victory... how I left you with a dying system...
Mouse: One last double-cross, sugah? -turns Megabyte's portal into a port to the web-
He would have won, too, if it weren't for the timely lost-game that forced the system to, well, reboot.
Played straight in season four, which ends on the mother of all cliffhangers, with Megabyte in control of the Principal Office.
This happened in a few episodes of season 1, with Megabyte's plans succeeding at first until Bob & co manage to save the day. Hexadecimal came the closest, actually, in the episode 'Medusa Bug'. Bob was the only one immune to the bug because of his Guardian status, but everyone and everything else in Mainframe got turned to stone. Then he pointed out to Hex that she had just brought complete and total order to the entire system. Needless to say, she was disgusted, and immediately reversed the effects of the bug.
Not to mention the end of season two, where Bob and Megabyte end up in an Enemy Mine situation, trying to save Mainframe from being devoured by the web. Naturally, once the immediate danger to the system was under control, Megabyte double-crossed Bob, shooting him into the web. (Bob survived because of his Guardian code, but no one would know this for sure until late in season three.)
In the middle of season three, the User manages to defeat Enzo and win the game. (The only reason he, Andr A Ia, and Frisket weren't nullified is because they were able to convert to gamesprite mode.) Matrix got his payback towards the end of the season when the Users wound up in Mainframe thanks to the system's instabilities.
In the Ruby-Spears Mega Man cartoon, while his primary goal wasn't achieved, Wily made off with the money from robbing the citizens in "Crime of the Century" and the money from selling a shrunken Washington D.C. in "The Incredible Shrinking Megaman". If you want to get technical, he also got all the money from selling Fun World tickets.
In The Dreamstone episode "Argorrible Attack", the Urpneys actually succeed in giving the majority of the Land of Dreams nightmares (a small time victory, but exactly what Zordrak wanted). The heroes try to give Viltheed good dreams in revenge, and it actually proves somewhat ineffective. Though granted after that they decide to just beat the crap out of all of them instead.
They do this again in "The Dream Beam Invasion", shrinking into the Noop's dreams and sabotaging them for one night. While they are foiled the following attempt, Frizz and Nug still manage to sneak into a dream and succeed. An angry Rufus, Amberley and Albert shrink into the dream seeking retribution, but change their mind when the Urpneys start growing back inside the dream, allowing them to retreat (albeit just above a lake...).
Also in "The Spidermobile" Blob and his gang effortlessly overpower the entire Wut army and capture the Dreamstone (along with Rufus, Amberley and Pildit) using the aforementioned machine. For once they do not screw things up, it is Zordrak and Urpgor instead that lose the stone, something Frizz and Nug find to be Actually Pretty Funny.
Zordrak also succeeds in sending nightmares in the pilot and "The Nightmare Stone", while Zarag manages to do so in "The Substitute". It is also implied Argorribles actually make their way past the stone's barrier and succeed in giving nightmares on a frequent basis, just in very few numbers.
Four Popeye cartoons have Bluto/Brutus winning, but it was all precipitated by Popeye himself:
In Hospitaliky (1937) and For Better Or Nurse (1945), Popeye and Bluto are both jockeying to severely injure themselves so they can get close to nurse Olive at the hospital. Popeye ends up force-feeding his spinach to Bluto, who delivers the necessary punishment to send Popeye to the hospital. I Bin Sculped (1961) has Popeye and Brutus vying to be Olive's model for a statue depicting a tired, beat-up specimen. Again, Popeye gives Brutus his spinach. He does so again in Round The World In 80 Days (1960) as a means to win a global race (Brutus socks Popeye on the chin and it sends Popeye circumnavigating the globe to the race's finish).
Bluto: (after he and Popeye both miss getting hit by a train) Ya runt! Now neither one of us is goin' to the hospital!
Popeye: Oh, yeah? Well, one of us is goin' to the hospital...(takes out spinach) and it ain't you!!
Brutus actually comes up smelling like a rose at the end of The Day The Ball Went Over (1960) without even laying a finger on Popeye, whose nitroglycerine-laced ping-pong ball explodes on him when he intended to have it explode on Brutus.
Olive: Is there anything special you'd like, Popeye?
The Jake and the Never Land Pirates hour-long special "Jake Saves Bucky" has Captain Hook challenging the protagonists to a race for ownership of the Buccaneer. He actually wins, only to lose it in the second half because a loophole in their contract that he didn't want to show them allowed them to reclaim it if they completed a certain task by sunrise.
The Jem episode, "The Day The Music Died" has the Misfits taking over what's left of The Holograms and The Stingers after Riot tricks Jem into taking a cruise with him to Mexico and then becoming stranded on an island. Once Jem is found and returns home, Pizzazz quickly gives control of Starlight Music back to Jerrica/Jem without a fight because all the money she made in her absence went right back into taking care of the Starlight Girls and maintaining Starlight House.
Peg Leg Pete did win one bout against Mickey in the Classic Disney Shorts. "The Barn Dance" ends with him winning Minnie's affections after being unimpressed by Mickey's poor dancing skills. The mouse is in tears.
On January 5, 1971 in Martin, Tennessee the Washington Generals defeated the Harlem Globetrotters 100-99 ending a 2,495-game winning streak and earning Harlem its only loss between 1962 and 1995. The Globetrotters got so involved with their comedy antics they neglected to notice how much they were trailing by in the normally pseudo-competitive game against their long time comic foils. A possibly legitimate attempt to rally back came for naught when Meadowlark Lemon missed a last second shot. The crowd in attendance was stunned with several children breaking out in tears.