The Mark of Kri and its sequel, Rise of the Kasai, feature dismemberment and some brutal animations despite what the stylized artwork may suggest. Alien Hominid has its moments. Carmageddon is pretty graphic if you run over pedestrians. They may not be the most violent games thus far, but if Call of Duty and Silent Scope can make it in the top 100, I don't see why those games can't.
Edit:
I just looked at the top 10. While MK more or less brought the blood and gore factor to the forefront as well as being an on-going series, I found most of the fatalities so over-the-top that it's funny. I found Phantasmagoria to be more disturbing; not only was it graphic, but the fact that the victims were helpless.