I can't recall any books or fics that have really seriously disturbed me, but I can say I've written one or two that readers found disturbing. The close I've come to feeling particularly bothered by books is when I encounter stream-of-consciousness writing... be it good or bad, the disjointed trip through someone else's head tends to trouble me a little because I never know where I'm going to land.
It's worth noting that the aforementioned works I authored which people found disturbing were written in that format.