Sure. Thor and Hercules have clashed multiple times in different comic series. Their fights often stem from differences in power, ideology, or the circumstances of the story.
Thor would have a good chance of winning. His powers are not only physical but also magical. He can summon lightning storms and has the ability to heal himself. Darth Vader, while a formidable opponent with his dark side powers and lightsaber skills, is still mortal. Thor could withstand a lot of damage and keep coming back at Vader. Also, Thor's hammer can only be lifted by those worthy, which gives him an added layer of protection. If Vader were to try and grab the hammer, he would not be able to, and Thor could use that moment to strike.
Thor first appeared in 'Journey into Mystery #83' in 1962. In this story, Dr. Donald Blake, a disabled medical student on a vacation in Norway, discovers a mysterious cane. When he strikes the cane on the ground during an emergency, he is transformed into Thor, the mighty God of Thunder. This was the start of Thor's adventures in the Marvel Comics universe.