Prestige Classes are a tool. Find the ones you want to use, and fit them to your campaign world. Prestige Classes are neccessarily generic, in most cases, to allow them to be brought into a specific world or setting by a DM. You can further specialize or explain the classes yourself, in your own world.
For example, taking the Assassin class, and a way I would modify them... In many worlds, ressurection magic is accessible and practical, especially for the more powerful people in the world. What is the point of assassinating someone if they will simply be ressurected upon the morrow? So, to counteract this, a specialized group arose, the Assassins. The Assassins recieve special training to eliminate targets and are shown ways to kill that will prevent ressurection magics from functioning on a target that is killed by the Assassins Death Attack. At 10th level, the Assassin recieves a "Final Death" ability similar to that of the Hunter Of The Dead, only it works on living targets. Upon reaching 10th level, all of the Assassins attacks, not just the Death Attack, prevent ressurection magic from functioning. Because of this ability, all who seek to eliminate someone permanently, go to the Assassins Guild.