Loved the "psychic crime mystery"-sidequest in Dungeon Siege 2. First, you need to learn how to communicate with ghosts, then speak to the dead butler, find clues, learn the story of betrayal and murder and apprehend the perpetrators. It wasn't really that interactive, you basically just walk around and click on items and people. But it's well presented and a nice take on a sidequest that doesn't involve killing X number of Y or killing Z to have it drop B which you bring back to A.
There are almost certainly better sidequests, but this is the one I think of off the top of my head.
There are almost certainly better sidequests, but this is the one I think of off the top of my head.