My favorite campaign that I have played in was a Legend of the Five Rings game that retold the events described in Way of the Shadow. None of us had read the books so our immersion into Rokugan was very interesting. I really enjoyed my Shugenja Isawa kaeteru, a void mage.
My favorite campaign that I ran is the Doombringer story for my homebre setting. It was a prehistory game, set before the written history of the campaign world. It allowed me to play with themes on a more primal level, and was actually a big departure from the normal games-while still making sense in the context of what the players already knew.