My first thought, though I don't know if this is what you mean, is the villain in the movie Gladiator. I know it's not a book, but that was a character who was just destroyed by life, and I felt so sympathetic for him that I ended up really disliking the movie because he was so vilified.
Another example that almost works, but doesn't quite, is the villain in a manga series called Monster (one of the best stories ever, btw). He only sorta counts because one of the great mysteries is whether or not he's truly evil, as in if he was born evil, or if the horrible events that happened to him throughout his life caused him to become something that should be pitied instead of hated. That dichotomy was awesome, and I won't tell you how it turns out, but that question of whether or not he was actually more of a tragic character than an evil one was probably the coolest thing about the story.