Heroes of Horror, an excellent book all around, has a taint system to it. Similar to Oriental Adventuers and Rokugan, Characters acquire Taint by committing unwholesome (not necessarily evil) acts, interacting with tainted items, or going to tainted places. Taint would have a noticeable game effect as it accrued, depending on what kind it was.
I feel their system is a bit over-complicated, bifurcating Taint into a physical and a mental category, with seperate game effects for too much of each. But I really liked some of the side options that went with it, including prestige classes that were attainable only when characters got a certain amount of taint. In particular, I liked the idea of Taint replacing alignment, so persons who committed evil deeds weren't evil per se, they had a high taint level. Abilities changed too; for example Paladins could detect taint and smite taint. Especially in a Cthulhu-esque campaign, it's a nice alternative to the rigid alignment system.