I'm thinking they are only in quest-specific dungeons, as that's the only time I'm ever seen one in game. If it's not tied to the Companions in some way, the werewolves just don't show. Or am I missing some runing around in the woods somewhere?
Sadly no. It seemed to be something Bethesda overlooked, or maybe they didn't want you showing up to the companions and being like, "Err.... No, thats fine, I'm already a werewolf...".
There is one... but he's not really wild. Depending on how you complete "Ill Met by Moonlight" there can be a werewolf who pops up from time to time. Besides the ones in cages, he's the only one.
Well, i found some in the Rift, close to the east moutains that lead to Morrowind. Not sure if my game is special or they were just inside cages and somehow went out of them, them ran out of their cave and kept running until i killed them...
I think they could have added wild werewolves after the companion quest where you become one. This solves the problem of being infected with their lycanthropy.