I'd say the American Civil War also had a good and bad side. One could make a weak argument that the South was fighting to defend its culture and way of life from domination and exploitation by the North, but I've heard the same argument about World War II Japan.
Another possible candidate is the Vietnamese Invasion of Cambodia, 1979-1980 (whatever Vietnam's true motive for invading, the Khmer Rogue were clearly worse, and deserved to be overthrown).
Well considering China, the West, and the rest of Southeast Asia all provided covert support for the Khmer Rouge I'd venture to guess that it was far from obvious which was the clear good side. It was more a war between a bad side and a horrid, atrocious, despicable side.
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