The partisan movements in Nazi-controlled areas during World War 2 gave regular forces information and helped them with acts of sabotage that made their military operations much more efficient and less costly.
According to the folks at the Axishistory forum, the largest European resistance movement in proportion to the size of the population was, surprisingly, in Albania (6.5% at its peak). Second was Yugoslavia, Greece and Poland are tied for third place, followed by USSR, France, Italy and finally Bulgaria. Other movements did exist, but were much smaller.
In Germany itself, the White Rose (a nonviolent resistance group led by students) opposed Nazi rule after the disaster of Stalingrad.
The Werewolves, pro-Nazi partisans (mostly ex-Hitler Youths) who operated in occupied Germany.
The Polish Home Army was not just a Ragtag Bunch of Misfits, but a full-blown government operating in conspiracy. They had their own judicial system, educational system (extending from primary schools to universities), hospitals, arms factories producing the indigenous Błyskawica submachine gun and intelligence service operating in other countries. Its political activities ranged from assassinations of German officials to taking care of families of deceased soldiers to providing Jews with false documents. Downplayed in that the Home Army was technically an extension of the Government in Exile and operated under its orders. The two politically distinct groups, the National Armed Forces (nationalist) and People's Army (communist), play this trope straight.
On a sidenote, virtually any significant pre-war political organization, from natonalists to farmers to communist had its 'own' resistance organization.
In outlying regions with mixed populations, the Polish Home Army was also seen as The Empire by the local Ukrainian, Lithuanian, and Belarussian nationalists. In many cases, a four-way conflict developed as the Poles fought the nationalist La Résistance belonging to whichever was the major "other" ethnicity in the area, while they both fought the Germans AND the Soviets at the same time.
The Greek National Liberation Front was also heavily organized, with its own goverment, polls, and a popular army of thousands essentially controlling almost all the rural areas of Greece by the end of the war, and had already set up infrastacture like schools and health care for the places they freed BEFORE the war was over, and did heavy fighting with the Germans holding essential reinforcements from the East Lines.
Italy had the biggest partisan movement of any Axis power. That was because Fascism got its supporters from the upper-middle class, who considered it a way to control the lower class. Needless to say, Fascism wasn't seen in a positive light by the farmers and workers who made up the majority of the population.
One of the most notable things of the Italian resistance was the success it enjoyed, at one point conquering a number of towns and creating temporary republics (including one near Mussolini's own hometown), before launching an insurrection in every single town and city still occupied when the Allies' spring offensive in Italy broke through the Gothic Line and prevented the Germans and Fascists from even attempting to use the Po river as a last line of defense. They also had their own weapon production of an original design, the Variara submachine gun (the only ones doing so besides for the Polish Home Army).
Second Sino-Japanese War saw several million men die in uniform, or bits of it, but many also died fighting the Japanese out of it. While it's true that there were communist cells in the occupied areas, these co-operated with the occupation authorities to help them root out all the non-communist ones. The Communists also refused to actually do any fighting, except for that one time when Stalin ordered them to in 1940 to save the Guomindang's hide, since they wouldn't have minded Japan winning (since it would mean them winning the Chinese Civil War by default) and wanted to build up their strength so they could start the Civil War up again later if the Guomindang survived.
Norway did not get an exceptional amount of publicity but both held out longer that France from invasion to defeat/surrender and had an active resistance going throughout the entire war. Granted it was not very violent, but it did manage to smuggle out its entire gold reserve, blow up ships loaded with heavy water headed for Germany, and carry about half the country's Jewish population over the border with Sweden. The other half were scooped up very suddenly, with not even Quisling being told about it. Then there is also how the executive, legislative, and judicial branches of the country all refused to collaborate.
Zigzagged with a large number of movements during World War II (and to some degree, World War I), which were both La Résistance and Les Collaborateurs depending on your point of view. With the empires at war, many independence movements sided with the empire fighting against their own overlords. During World War I, Finland and the Baltic States gained independence from the Russian Empire (and its Soviet successor) with the support of the Germans. During World War II, many Croatians, Slovaks, Balts, and some Ukrainians cooperated with Nazi Germany against their Serb, Czech, and Russian oppressors. A large number of Southeast Asian and Indian independence leaders cooperated with the Japanese against their British and Dutch colonial masters.
Stay-behind units organised in case of a Soviet invasion of Europe. During World War II the Home Guard Auxilary Units in Britain carried out a similar function.
Being in a Home Guard Auxilary Unit was a heavy burden, because if your unit was actually activated (which would occur automatically if your town was occupied) the first job was to ensure security by killing the only other man who knew who the members were: The local police constable, who was invariably a close friend of all the members and trusted them enough to kill him if needed.
Several resistances against undemocratic governments in Latin America and South America qualify, markedly in Brazil the MR-8.
The MIR/Manuel Rodriguez Patriotic Front in Chile and the Montoneros/People's Revolutionary Army in Argentina might qualify as well.
During many wars local civilians were provoked by the incredible presumption of passing soldiers into becoming this. As if they failed, they would be subject to worse Rape, Pillage, and Burn than before, if they succeeded they would end up becoming like their persecutors and if they did nothing they would simply be ground down underfoot, it was a tough choice. Effectively it was La Résistance against both sides for pure self-preservation, but the chief target would be the nearest army.
The Spanish Civil War serves as both an example and a subversion. The Nationalists thought of themselves as La Résistance to the leftist government, but were much better organized and prepared for war than the leftists (Loyalists). This makes sense considering that the Nationalists controlled most of the army, and had the direct backing of Hitler and Mussolini. As a result, the Loyalist government itself was reduced to a Ragtag Bunch of Misfits who frequently fought amongst themselves (in some cases, particularly for the Stalinists, the faction fighting was actually more important than fighting the Nationalists—many Loyalist offensives never got off the ground because important officers were detained and sometimes executed by the Stalinists in the name of ideological purity).
The anarcho-syndicalist uprisings in Catalonia was this on the leftist side, though (and certainly not "Loyalists", as they fought for the complete dismantlement of the state apparatus and had strained relationships with the rest of the Republican side). Under the guidance of the FAI-CNT the citizen rose up against the Nationalists and fired off the shots for an anarchist insurrection, allying only with the Loyalist government as a sort of "the enemy of my enemy" deal. Boy did that bite them in the ass later with the Stalinists.
The Arab Spring. Protests and revolutions have occurred in Tunisia, Egypt, Algeria, Yemen, Libya, Morocco, Bahrain, Syria, and Iraq and Iran.
Haiti is an entire nation formed out of the success of a slave rebellion—a rare (indeed, unique) feat.
Finnish Civil War 1918 - both sides. The Whites considered themselves as the representatives of the legitimate government resisting the Communist Imperialism (which would have been true is they hadn't exiled, imprisoned or executed all the M Ps of the biggest party), while the Reds considered themselves as the sole defendant of the small guy against Capitalist oppressors (which would have had a bigger ring to it if the Finnish people hadn't shown through universal suffrage elections that they didn't like the communists). Needless to say, the Finnish Civil War was extremely bloody.
The Vendée Rebellion 1793-1796 in France. The Vendéens, who had initially welcomed the French Revolution, saw it quickly escalating off the hands and after the Civil Constitution of the Clergy and the execution of the King, decided they had had enough of this revolution stuff. They repulsed the Revolutionary armies, declared themselves as the defendants of the legitimate government and managed to evict the Revolutionary regime completely off the Vendée department. The mutiny was quashed in 1796 and ended in torrents of blood, but guerilla war continued until the end of the Napoleon's regime and restoration of King.
Hamas in Palestine, Hezbullah in Lebanon, Taliban in Afghanistan, the Muslim Brotherhood in Egypt, as well as the Iraqi resistance after the 2003 invasion. The first four organizations alternate between being La Résistance and a de-facto government. In case of the Muslim Brotherhood, they were de-jure government too until the Egyptian military stepped in again.
The Dog Soldiers, one of six military societies of the Cheyenne Indians, opposed peace policies during their ongoing fight against the settlers, and refused to be restricted to reservation land. They were an important part of Cheyenne resistance, but eventually were almost entirely killed off in the Battle of Summit Springs in 1869.