Ace Combat: These games often have a resistance movement on the ground aiding your efforts in the air.
Agent USA: Whenever fuzzbodies enter a city, the (normally randomly wandering) citizens start dropping crystals to try to fend off the fuzz menace. That's about as useful as they get, though, but being from a game from the early 80's, it's more help than one would usually get from games at the time.
Assassin's Creed: Brotherhood: Ezio Auditore builds up the Italian Assassins to become a resistance group against Rodrigo Borgia (aka Pope Alexander VI) and his son Cesare Borgia's control of Rome and Italy.
Assassin's Creed III: By the 1760's, the Assassin Order in the New World has been reduced to little more than two broken-down old men on a dilapidated homestead. It takes a determined Native American/English boy to kick them back into gear and rebuild the Order.
Bahamut Lagoon: Subverted Trope. This is a Squaresoft RPG, much like Chrono Trigger that while not called "Final Fantasy", certainly shares many similarities. The player characters are part of a resistance group, but as the game progresses, it seems that the Empire may not be all that evil, and a larger plot emerges. It is specifically mocked when another resistance group called "The Freedom Revolutionaries" is introduced, whose avowed purpose is to be cool and meet girls.
Crusader: La Résistance is actually called the Resistance, by both sides—they claim to have no need for a flashy, "formal" name. At most, they are referred to as the Global Resistance, which actually undersells it because there are cells offworld, too.
DMC Devil May Cry: In the world of this game, the world is run by demons who infect every facet of life with propaganda and attempts to control the populous. The resistance is "The Order", an organization led by a mysterious masked man who launches smear campaigns and attempts to subvert the demon's stranglehold on society.
There's the NSF, who're La Résistance to the US government and Majestic 12. Then there's the Luminous Path, who're La Résistance to Majestic 12 and Silouette, who're La Résistance to the "Vichy" French Government and Majestic 12. Finally, the Luminous Path are also La Résistance to The Illuminati, who're already on your side.
The novel Deus Ex: The Icarus Effect (taking place 27 years earlier) has the Juggernaut Collective, a cyberterrorist cell dedicated to fighting the influence of the Illuminati. One of their main financial supporters is Juan Ivanovich Lebedev, a wealthy industrialist. He is also the founder of NSF.
Played straight in this game and either straight (in the Rebel, Polaris and Auroran storylines) or not so straight (in the Federation storyline. The other storylines leave it open) in Escape Velocity Nova — one the founders of the Rebellion, Frandall, might or might not be the real head of the Bureau, who orchestrated the Rebellion for the sole purpose of drawing out potential opponents to their takeover.
In the backstory, anyhow. The Rebellion of Escape Velocity has gotten entrenched since its establishment, and the war is now more of an open conflict, starship-against-starship style, than an actual revolution. In other words, the game starts with La Résistance already having grown into The Alliance... and stays there.
Fire Emblem: Path of Radiance: Has this group, though it happens offscreen and is only mentioned when members of the Resistance join up the Liberation army.
Fire Emblem: Radiant Dawn: Has the Dawn Brigade led by Micaiah, though it quickly comes to resemble Joan of Arc pushing the enemies out the country, with the heroine being known from everyone, including the enemy, and hailed as a miraculous figure head, and joining and then leading the prince's army.
HAZE: The last Free Radical Design game, which is PS3 exclusive, revolves around this very trope. You start out as a sergeant in Mantel Global Industries' PMC (Private Military Corporation) with the purpose to fight against a rebel group, La Mano de la Promesa (or Promise Hand), that has taken over the fictional South-American region of Boa, and has been wreaking havok by ethnic cleansing, crimes against humanity and the like. In the end, it turns out that Mantel are the bad guys and you, the hero, end up joining La Resistance. (This has not been hidden as a spoiler because this, the main plot-twist in the game, is given away in all advertisements/reviews/the back of the frickin' box.)
Homefront: Has you being "recruited" into the titular resistance (or the home front) in the first level, right before the fighting starts. Not that you had a choice anyway, since the North Koreans weren't too keen on giving those.
Ikaruga: The Tenkaku. They are defeated by the Horai before the main events of the game occurs.
Ingress: The Resistance, the faction opposed to the Shapers and Exotic Matter, which are supported by the Enlightened faction.
Injustice: Gods Among Us: Has Batman and a team of heroes and villains going against Superman's regime, which uses fear to scare people into submission. The Justice League is divided between those who side with Bats, and those who side with Supes.
Jak II:Renegade: The Underground is a darker version of this, without actually falling victim to The Revolution Will Not Be Civilized. While they're willing to employ pretty much anyone who can help, deal with crime lords, and generally behave like terrorists, their leaders are still fundamentally nice guys who are doing the best they can; Torn left the Krimzon Guard rather than support Baron Praxis's continued canine-raping, and seems genuinely concerned for the people in the Slums who risk death when Praxis cuts off the water supply.
Making History: In the original Gold edition, resistance fighters will spring up and retake undefended regions in occupied territory. In the sequel, they'll rise up and try to fight a government that is doing poorly, or that they feel should not control their ethnic, national, or religious group.
The collective Reploid protagonists, aptly (and simply) called the Resistance, fighting against the government that wants to retire them.
Mega Man X: Command Mission had a "Resistance" to...the rebel army opposing the government. So it was pretty much The Resistance to The Resistance. Yeah.
Granted, both resistance movements were good at their core - the Resistance, which X aligns himself with over the course of the game, seeks to protect the people of Giga City from the Rebellion, which has Well-Intentioned Extremist faculty and simply wished for a Reploid-only domain independent of Federation politics. The latter are only seen as evil due to the fact that a few amongst the Federation unjustly branded them as Mavericks, forcing them to develop weapons in order to be heard and acknowledged. Not like the Mavericks Hunters haven't dealt with internal corruption before, though...
Operation Flashpoint: Had two different, but related rag-tag groups of civilians and former security forces employees fighting a Soviet invasion of their two fictional homelands during The Eighties phase of the Cold War. The aptly named Resistance expansion pack explored this whole trope in great detail and its whole narrative was seen from the point of view of the La Résistance's members.
Panzer Dragoon: Subverted in this series. Although they're the straight villains in the first and second games, the third and fourth games reveal that The Empire is corrupt, but ultimately the only thing protecting humanity from dangerous biological weapons — and members of the various La Résistance groups that have cropped up are shown to take a toll on the lives of innocent bystanders.
Paradox Interactive: In all of this company's grand strategy games you face the problem of revolution and rebellion, most notably by taking someone elses land and enforcing your rule on them but revolts can happen in your own country if you push the people to far.
Planetside II: The New Conglomerate sees itself as this, defending the liberties of everyone(but mostly businessmen) against the tyranic autoritharian rule of the Terran Republic. Depending on who you side with, they can either be seen as ruthless terrorists(for the TerranRepublic), noble freedom fighters or an inconvenience in the way to independence(for the Vanu Soreveignity).
Pokemon Mystery Dungeon Explorers of Time/Darkness: The future is grim and eerilystill, and a small band of resistance fighters led by Celebi is fighting the rule of Primal Dialga. Grovyle and the player were both members of La Résistance who were sent back in time to try to prevent Dialga from going Primal in the first place.
Quest for Glory II: There's supposedly an underground group opposing the totalitarian regime in Raseir, whose offscreen help you receive at the climax.
Rage: La Résistance is featured as the generic "Resistance" opposed to the similarly generic and undeveloped Evil Empire by the name of "The Authority".
Re VOLUTION: Jack Plummer eventually joins up with a group opposing The Corporation. This group is called the Resistance.
RuneScape: This game is home to Morytania, land of the dead. This is a horrific and dark place, ruled by vampyres who oppress the living inhabitants of the land and require them to pay 'blood tithes'. However, there is a resistance force known as the Myreque. Unfortunately, the odds are not in their favour, at least when the player first meets them.
The Saboteur: Has you play an Irish ex-mechanic/driver who joined the French Resistance about three months after the Nazis occupied France. You'll find the bulk of the resistance, the Foreign Legionnaires most especially, to be badasses.
Jim Raynor (and the Magistrate) are first rebelling against the Terran Confederacy, and, after its fall, against their former partner turned Emperor of the Terran Dominion.
In the novel StarCraft: Ghost: Nova, the titular characters wealthy parents are murdered by another resistance group, opposed to the Confederacy. Her first task as a Ghost operative under the Mengsk regime is to eliminate the cell that ordered her parents' murders. Apparently, after ascending to the throne, Mengsk becomes even more ruthless to various resistance groups than the people he overthrew.
In the game's backstory the Klingons conquered the Gorn Hegemony on grounds that its leadership had been heavily infiltrated by the Undine. There are several mentions and, in the Klingon storyline, appearances, of Gorn resistance fighters.
The Reman Resistance under Obisek is fighting to free their species from slavery under what's left of the Romulan Star Empire, which is now a military dictatorship led by Empress Sela and the Tal Shiar.
The Romulan Republic starts out as a rag-tag bunch of rebels headquartered out of a flotilla, hounded by the Tal Shiar. They cease to be this trope by the end of their first story arc, when they establish themselves on Dewa III — renamed Mol'Rihan ("New Romulus") — and manage to establish alliances with the Federation and the Klingon Empire, and by the end of the last Romulan-modified storyline, they are well on their way to being the dominant power in Romulan space.
Steel Panthers allows you to set up battles involving various resistance movements from World War 2 to the modern day.
The Bora Mining Guilds in Tachyon: The Fringe, opposing the expansionist efforts of the Galactic Spanning Corporation into their space. Bora themselves are descended from a radical political movement at the end of the war in the Sol System, who chose to leave the system for the great unknown instead of submitting to the new government. Centuries later, they are rediscovered, and the Mega Corpss decide to claim their mineral-rich region for themselves. How? Why, Loophole Abuse, of course. In their rush to leave Sol, and as protest to the new government, they didn't officially file a claim to their new region. Thus, GalSpan can officially move in and take the area. The free-spirited Bora couldn't give a rat's ass about what Sol or GalSpan can "officially" do and won't give up their homes. The game plays Your Terrorists Are Our Freedom Fighters to the fullest, as it allows you to choose one of two branching paths: Bora or GalSpan. When fighting for Bora, you are fighting the soulless corporation who doesn't hesitate from blowing up hospitals or civilian colonies for profit. When signing up as a mercenary for GalSpan, you fight terrorists who constantly sabotage the efforts of a progressive corporation to improve everyone's lives.
Sunrider: The player character, Kayto Shields, is the leader of the only survivors of the Cera Space Force.
Tears to Tiara 2: The Barcid Party is one, trying to resist the Holy Empire. Under the leadership of Enneads, they tried to do it peacefully by appealing to Imperial Law and reporting transgressions of Imperial governors, tax collectors, and soldiers. But as it doesn't really work they're always been planning a rebellion.
Trapt: Heavy taxation, starvation, and general mismanagement of the kingdom has caused the populace to rise up against the old royalty. Unfortunately for them, the player is one of them — Princess Allura, the heir apparent. And since the game begins with you inheriting the terrible, demonic powers of The Fiend (aka Satan), these particular rebels do, indeed, get stabbed, burned, skinned, tortured, and worse...