Code Geass is a prime time example of the useless-and-only-an-annoyance-kind of La Resistance until Lelouch turns them from a bunch of butthurt kids playing guerilla against the Britannian Empire to a fully organized and highly deadly army with victory after victory as its signature (that doesn't mean they're error-free, as we painfully find out in the Euphemia Massacre Incident and the following Black Rebellion).
Lelouch is literally considered the god of rebellion in the Pantheon.
The Joui from Gintama, who set out to take down the Amanto even if it meant going out into an all-out war with them. They failed. However, Katsura is the only one that makes an attempt to carry out any of the original group's ideals after that failure (and even then, it's kind of laughable); Gintoki decided that fighting stupid enemies was pointless and dropped out, Takasugi became a Nietzsche Wannabein order to avenge the death of his teacher, and Sakamoto got a day job.
Tends to show up in Leijiverse a lot, particularly in Arcadia of my Youth and Space Symphony Maetel.
One Piece has the Revolutionary Army, an anti-government faction directly opposed to the World Government and led by none other than Luffy's father, Dragon. So far they haven't actually appeared often, but they'll certainly be more important down the line.
Romeo X Juliet has the followers of the Capulet family, fighting against Lord Montague.
In Saint Beast, the rebellion against Zeus is lead by the six Saint Beasts until four of them end up Brainwashed and Crazy leading to its failure and Judas and Luca taking the fall for it.
Saint Seiya: The Bronze Saints during the Sanctuary Arc.
Team Dai-Gurren from Tengen Toppa Gurren Lagann. Not only do they rebel against Lord Genome and his forces, but also the millennia-long reign of the Anti-Spirals.
The Secret of Twilight Gemini: After more than three hundred years of civil war, the remnants of the Geltic Tribe continue to fight the oppression of the Igo Tribe, who drove them from their ancestral home. Lara and her friend, Zora, lead them in the quest to unify their people and reclaim their homeland. With help from Lupin, of course.
The Secret Avengers and Typeface's Gang during the Civil War.
Marvel Star Wars has a resistance on Solay, trying to topple a pro-Empire king. They call on the Rebel Alliance for help after Endor, but it turns out the head of the resistance had secretly also been pro-Empire - soon after the king is deposed, the Imperial fleet comes in and imposes martial law, controlling the system directly.
Played with interestingly in the Star Trek graphic novel The Modala Imperative. Captain Kirk and Spock help the resistance on the planet Modala break up a vicious dictatorship; a hundred years later, the Next Generation crew arrive to help celebrate the anniversary of the original coup and discover the erstwhile rebel leaders are now beating back an uprising themselves. Then suddenly everyone must put aside their differences when the realBig Bad beams in - the Ferengi, who had sold the original dictatorship their weapons and have now come to collect from the current rulers.
Also in the current comic book series "Year 4", continuing where the original series ended, the rebels attack with the crew present (and later kidnap Kirk) in order to get the Federation to intervene in their conflict...at the same time as the government tries to blow up the Enterprise, to get the Federation to intervene in their conflict.
Judge Dredd has personally led resistances on a number of occasions, such as against Chief Judge Cal ("The Day the Law Died"), the East-Meg occupational army ("Apocalypse War") and the Dark Judges ("Necropolis").
The Picaros from the eponymous The Adventures of Tintin adventure. Tintin demands that their revolution will not see a drop of blood shed, much to the humorous consternation of many involved. Including the dictator being overthrown.
In Forever Evil, with the Justice Leagues missing, pockets of remaining superheroes are trying to fight back. The Teen Titans are one group, with the main event series following Lex Luthor's newly minted Legion of Doom.
A better example are the Changelings, who thanks to Cadance are now symbiotic instead of parasitic and protect ponies from Discord. They're also immune to Discord's magic thanks to Cadance. Cadance once ruled them and their kingdom Avalon was about the only place safe from Discord. While she was eventually killed and it destroyed, the Changelings are still protecting ponies from Discord and Discord hasn't managed to infiltrate them either.
The Shining Armor Arc has a group of Deer opposed to Makarov and the Hooviets, led by their true goddess, Mother Deer. The group eventually allies with Shining and Cadence's forces.
Nights Favored Child has the Harbingers of Dawn (or "Dawnists", for short). They're mostly in the background right now, but Twilight's late parents were members, as is Miss Loch, the head of the orphanage Twilight grew up in.
My Hostage Not Yours: The third story, where Zim and Gaz go full-scale Villain Protagonist and start taking over Earth, sees Dib form a resistance with his classmates, which he simply calls "the Group" (Gaz lampshades how lame it is). There's also the Swollen Eyeball Network, which proves to be much more effective. Both fail, though the epilogue reveals that resistance groups continue to pop up worldwide for years afterwards.
Apocalypse: The Haters, which is One Nation Earth's name for underground groups of persecuted Christians during the Tribulation in this film series.
The Army of Crime: The French film is all about La Resistance, being set in Second World War France during the German occupation. Based on a true story.
The Matrix: Has a population of humans attempting to strengthen numbers by freeing people imprisoned in a virtual simulation created by advanced artificial intelligence using them as a fuel source.
Monty Pythons Life Of Brian: Hilariously parodied, where there's more than one resistance, they don't do anything other than discuss things around a table, and the only time they actually do something they screw it up by arguing with each other. "THE JUDEAN PEOPLE'S FRONT? Splitters!" Even better if you take it as a comment on the state of left-wing and Palestinean movements in that time.
Pimpernel Smith: This film, which is The Scarlet Pimpernel in WW 2, with a stuffy English professor running a resistance network rescuing Jewish and other persecuted prisoners and funnelling them to Britain.
Red Dawn 1984: The school kids who head off into the mountains to fight the Evil Empire in the movie are a perfect example of this trope. Readers here may be more familiar with it being referred to as a documentary on one of the radio stations in GTA Vice City. ''Wolverines!'
Red Dawn 2012: The same goes for this remake except instead of the Soviet Union, it's now North Korea overrunning the United States.
South Park: Bigger, Longer & Uncut: Has a French-themed La Resistance (pictured) being composed of the children of South Park rebelling against their parents in the hope of rescuing Terrence and Philip from being executed. They even had their own song, as well as a Dark Reprise.
Valkyrie: Unusually for this trope, this movie focuses on the German resistance during World War II rather than that of the occupied countries.
Zwartboek (Black Book): Deals with the Dutch resistance in the Nazi-occupied Netherlands during World War II.
The Dragon Lady becomes a resistance leader, fighting the Japanese invaders in Terry and the Pirates. Terry and Pat are frequently dragged into her plots. Other resistance leader, such as the Blue Tiger, also feature prominently.
The Resistance is a reoccuring faction in Kaizers Orchestra's song universe, especially in Ompa Til Du Dør, which is set during WW 2.
Dark Sun has the Veiled Alliance which provides most support in areas of non-defiling magic and helping slaves to escape.
Forgotten Realms got Randal Morn and his supporters conducting guerilla war against Zhentarim occupation of Daggerdale for about 16 years (1353-1369) before Zhents were finally kicked out and he became the official ruler. Calimshan has Janessar, the group with strongholds in Marching Mountains that works to support common folk and free slaves.
Magic The Gathering has the Mirran resistance struggling against the forces of New Phyrexia. They know the odds are against them and that they are vastly outnumbered, which is reflected in the greater number of Phyrexian cards in the "New Phyrexia" block, but they refuse to lay down and give up.
In Return to Ravnica story, the population who are not part of the ten guilds are starting to take up arms against those guilds. Considering that the ten guilds include The Mafia who'll bleed people (of their money or life) dry, Mad Scientist guild who should be maintaining the city's infrastructure but aren't, sneaky spy guild, an entire clan of barbarians and so on, it is understandable why the populace are angry.
The Champions scenarioThe Sands of Time features an extradimensional species, the Orisha, who are ruled by a theocracy set up by one of the scenario's villains. There is also a rebel movement of heretics, though not too surprisingly, they're a little nuts. Still, they heretics are a resistance force who can help the PCs against the evil government of their world.
In Les Misérables, Les Amis de l'ABC (whose name has "the friends of the downtrodden" as a second meaning).
Later, on post-Scratch Earth, adult versions of Rose and Dave lead La Resistance against the forces of Betty Crocker/the Condesce, who far in the future has taken over everything. Unfortunately, they are doomed to fail, but they go down fighting and take out some of her top puppet leaders in the process.
In Sluggy Freelance, when demons invade the Dimension of Lame, the humans put together a resistance movement. Unfortunately, since it's a very lame dimension, "resistance" consists mainly of hitting the demons with pies. And most people in the dimension even think thatmakes them no better than the demons who kill them for fun and eat their souls. It's a very, very lame dimension.
The Resistance in The Order of the Stick is composed of two of the main characters and a bunch of Azurites whose main goal is to fight Xykon's troops who are currently occupying Azure City after having won a huge battle and taken over the city. Eventually, Haley and Belkar leave the group, leaving the paladin Thanh in charge of the Resistance.
There are also two other factions, one claims The Order corrupted Lord Hinjo, and the other thinks Hinjo was responsible for the death of lord Shojo, and the Order were cohorts. The three groups don't get along at all, until united due to a makeshift prophecy.
As of strips 825-827, Redcloak has successfully killed every member of the resistance except for Niu, and destroyed their base.
In Terra the Resistance want to stop the war between the humans and Azatoth because the unaligned races and civilians are getting it in the shorts, and because factions on both sides (the military-industrial complex in the UEC, and the Shadow Cabal in the Asurian Empire) have ulterior motives for continuing it. The Resistance formed out of an alliance between several militias and resistance groups.
The Chaos Timeline has various. Spaniards against Republican France, Germans against Russians and Italians, (again) various against the Socialists.
In Decades of Darkness, there are several ones fighting the expansionist, slaveholding *USA, like the Velvet Underground in Pennsylvania, Mexican generals like Juarez, and Eunuco Mitchell (it's a pseudonym). Unfortunately, none have prevailed.
In Shadowhunter Peril, the main characters are forced to become the Resistance because it's either fight back or die. They actually end up doing a pretty good job, even amassing a giant army of phoenixes and raining a fiery storm down upon the Big Bad's capital city. Currently they're in the middle of the final battle, so there's no way of knowing who's going to win, especially with Lilith and Valentine still alive.
Taking from its source material, the Rebellion in The Gungan Council have been revived several times to restore democracy after the Galactic Empire came back.
In Victoria, a story from The Wanderers Library, the Earth has been taken over by… something. What exactly is never made clear, but they're opposed by the Human Resistance Group, who uses superior numbers and technology to fight back. Whether it eventually succeeds or fails is never elaborated upon.
Lampshaded in the Justice League by Green Lantern in "Hearts and Minds." "There's always a resistance, isn't there?"
The Resisty from Invader Zim were a resistance movement against the Irken Empire. To their credit, they very nearly destroyed the Massive, but only because Zim had seized control of it and had removed its defenses. Also in Invader Zim is the Swollen Eyeball Network, a group of genre-savvy conspiracy theorists who have foiled alien invasions. Naturally, Dib is a proud member, codenamed Agent Mothman.
The Burners in Motorcity, against Abraham Kane of Detroit Deluxe.
The backstory of one chef in Ratatouille involved running guns for one of these. "Which one?" "He won't say - apparently they didn't win."
On The Venture Bros. the Orange County Liberation Front is a resistance movement trying to take down the Brisby "empire", an obvious Disney parody.
The second season of The Venture Bros also features a lame but zealous resistance to Baron Ünderbheit's iron fisted (and jawed) rule in Ünderland. One of their proudest achievements is sneaking a cat hair into his drink.
The first season of W.I.T.C.H. features the rebellion against the Big Bad Phobos, with Badass Normal Caleb as the young rebel leader. After Phobos is defeated and imprisoned, the situation is inverted during season two, with a small band of Phobos' remaining loyal troops attempting to overthrow the benevolent queen Elyon.