I'm basing my question off of this list: http://en.wikipedia.org/wiki/List_of_murdered_popes
Because that's simply going by wikipedia titles.
We know very little about the lives of early popes. What we have is mostly rumor and unsubstantiated claims.
Just off the top of my head, Pope Clement I (92-99) was thrown into the black sea with an anchor around his neck, Pope Stephen (254-275) was beheaded on top of his throne, and Pope John VII (705-707) was supposedly beaten to death. There's not a ton of solid evidence for any of those things, which is part of the issue.
A rewording of the question would be "Why did 900-1000 have such an unusually high number of murdered popes?"
To that question I can't account for it in full, although I can explain at least some of it. Quite simply, there were more popes in that time period. The later one gets, the less popes there are. The 20th century had only eight popes, while the 10th century has twenty-two.
There are a lot of other factors (political climate, etc), but I'll leave that to someone who knows a bit more about early papal history.