I read on Wikipedia about the Werewolf group and a few small units of SS soldiers who were still fighting during and after the capitulation. Was there any larger kind of pro Nazi resistance movement against the Soviets or the Western Allies?
There was no organised, large scale resistance movement against the Allied occupation either during the final months of the war, or after the German surrender. However, there was a small scale ad-hoc partisan campaign carried out by decentralised forces and some elements of the Werwolf units which had been specially trained for that purpose. However, the propaganda surrounding the Werwolf units lead the Allies to take a much harsher stance toward their occupation of Germany. Ultimately, German partisans ended up causing far more harm to German civilians than to Allied forces, both indirectly through harsher occupation policies and directly through reprisals by Allied forces.
The idea of partisan organisations was first mooted by German intelligence officers in 1943, and the idea found patronage in Goebbels and Robert Ley. The first SS-Guerilla units were set up in September 1944, and by October had come to be known as "Werwolf"" units. There is some controversy over where the name came from, but it seems to have been chosen both due to the connotations of werewolves in popular culture, and in reference to a popular novel set in the Thirty Years war, where a Saxon peasant organises a milita to hunt down and kill soldiers who killed his family.
Werwolf units were mostly composed of SS soldiers and recruits or conscripts from the Hitler Youth, whose fanaticism and capacity to be overlooked by Allied soldiers were dual advantages. The increasing militarisation of the Hitler Youth saw many young children issued anti-Tank weapons and marched off to the front, or told to wait until the enemy had passed before striking.
The Werwolfe were put under the command of Hans Prutzmann, who turned out to be rather incompetent and was more fond of showing off sabotage equipment to his friends than organising a mass resistance movement. His units first saw action on the Eastern front, where they gathered intelligence and attempted to conduct sabotage behind Russian lines, although most units were destroyed before doing any real damage. Units in Berlin were more successful, killing a number of Red Army soldiers and driving a wedge between the civilian population and occupiers.
In the West, Werwolf operations were similarly unsuccessful. Operations in the staunchly Catholic, anti-Prussian Rhineland were a complete failure, and most operatives were captured or killed without taking any action. In some areas, fighting erupted between groups of civilians in attempts to stop the sabotage or demolition of factory equipment or property. When American troops arrived in Erkenschwick they discovered "a minor civil war" between pro and anti-Nazi underground groups.
Further east, units laid mines and traps, and conducted ambushes. However, while these units could cause annoyance, they were not able to pose a proper military threat. In the suburbs of Bremen, one unit of Werewolfe was caught by a British armoured car laying mines, and vainly opened fire with pistols before being mown down.
Resistance by civilians who were not formally part of constituted Werwolf groups was also a major problem. While formal Werwolf membership never numbered more than 6000, many more civilians took part in guerilla combat. In Wurzburg in particular, fighting against civilian units was so brutal that not a single fighter was left alive to formally surrender to American forces.
Partisans were also reasonably successful in assassinating German officials in occupied zones. The mayors of Krankenhagen and Kirchlengern were assassinated by Werwolf units, as were a number of Berlin policemen. In April, a Werwolf group came very close to assassinating the co-leader of the anti-Nazi movement in Augsburg. The most significant assassination was the murder of the Mayor of Aachen on the 20th of March.
All of these activities were played up by German radio propaganda, causing significant worry amongst Allied commanders. While the actual effect of these units was minor - the assassination of a number of officials in the occupation zone, five thousand kills at the most and extensive property damage - they loomed as a major threat in the perspective of the occupiers, who feared a protracted partisan war, and the creation of a "national redoubt" in the southern mountains and forests, where entrenched German forces would continue fighting.
One of the major proponents of the theory that Germany would continue to resist after the war was General Eisenhower, who wrote in August 1943 that:
It may well be that the German Army as a whole will never actually surrender and that we shall enter the country finding no central German authority in control, with the situation chaotic, probably guerrilla fighting and possibly even civil war in certain districts.
In April 1945, it was announced that Allied policy would be to hold all German officers as prisoners until the threat of Guerilla warfare had receded, and in March Eisenhower promised to execute all captured partisans on the spot. This led to an increase in battlefield executions by Allied troops, such as in the Hardt Forest where American tankers shot a number of civilians who had acted as guide for Wehrmacht Tank destroyers. Near Schweinfurt, a number of captured snipers were hanged by American soldiers. The British response was more measured, and British soldiers were not permitted to take part in the guillotinings of those who were to be executed. By the end of 1945, 100,000 civilians were also being held in internment camps by the Americans.
On an organisational level, the Allies found it difficult to set a policy for dealing with partisan activity. While the Allies were bound by the Rules of War, the implicit advice set out for commanders was that these could be contravened under specific circumstances. While the Allies did make contact with the resistance movements in France, Poland and the Low Countries to discover what mistakes the Germans had made in their occupation, from the outset they declared that they "should never as a matter of policy employ the more brutal methods of repression as practiced by the Germans."
As the Allies advanced across Germany, it was the Americans who dealt the most damage to civilian property and lives, although this can partially be explained by the fact that they faced heavier guerilla fighting than the British and Canadians in the North West. Towns and Villages were levelled, and the Americans threatened to shoot all male inhabitants of Stuppach in Wurttemberg if they didn't hand over a wounded soldier they were suspected of hiding.
We don't know if the Soviet occupation strategy was similarly influenced by a fear of partisans, but the brutality of their treatment towards German civilians made many think twice about offering resistance. The order was issued that any killing of a Red Army soldier by a civilian be punishable by execution and the destruction of their town or village. This was carried out on a number of occasions, such as near Plieschnitz in Silesia where 20 civilians were executed in response to the killing of a Soviet Officer. Anyone caught with a weapon or suspected of being a partisan was shot. After the war, a number of Red Army soldiers were killed by a sniper in the Berlin district of Charlottenburg. In response, the Soviets cut off food supplies to the entire district.
However, the brutality of Soviet treatment did end up inspiring some resistance that might not have otherwise taken place, such as in Kupp, where a member of the Hitler Youth killed a Soviet Officer who had raped his sister. In response, the Soviets destroyed the entire village, executed the family and numerous other civilians. By July of 1945, resistance had begun to die down, and the Red Army was able to exert a tighter grip over it's own forces, leading to a gradual relaxation of the severity of occupation.
The fear of the Werwolfe was also present in Czechoslovakia, where the memory of severe fighting after the end of WW1 was still fresh. This fear lead to a major incident on the 30th of July 1945 where an explosion in an arms depot in Usti nad Labem killed a number of Czech and German civilians. While the explosion was likely accidental, it was blamed on German saboteurs and German citizens were attacked by crowds who threw them in the Elbe. Several hundred were killed.
The effect of these repressive measures, while deterring partisans and making life difficult for the actual Werwolfe, was to cause significant resentment against the Allied occupiers, even amongst those who opposed the Nazis. Especially at such a delicate time when the Allied occupation had not fully established itself, this gulf between Allied troops and Germans made the administration of occupied Germany much more difficult than it could have been.
Ultimately, the unconditional surrender of German forces and Hitler's death made it very difficult to justify carrying on guerilla warfare for the Werewolfe and other unorganised troops. While sporadic attacks continued in the months after the end of the war and some units reportedly remained active until as late as 1947, there was never any concerted sabotage or guerilla effort after the war.
Bibliography:
Perry Biddiscombe, Werwolf!: The History of the National Socialist Guerrilla Movement, 1944–1946 (1998).
Mark Mazover, Hitler's Empire: Nazi Rule in Occupied Europe (2009).
Ian Kershaw, The End: Hitler's Germany 1944-45 (2011)
Roderick Watt, "Wehrwolf or Werwolf? Literature, Legend, or Lexical Error into Nazi Propaganda?". The Modern Language Review. The Modern Language Review, Vol. 87, No. 4. 87 (October 1992). pp. 879–895