In my games, gaining a prestige class has usually been a factor of meeting the requirements and just multiclassing in. I know that a number of PrCs involve special orders of do-gooders that one might have to petition for entry, but I rarely see myself using those at all. I know my PCs don't live in a vaccuum, but what fun is beating the badguy if there's an entire cadre of guys who are all higher level than you and far more devoted to the cause? The PCs still gotta be the stars of the show and I don't need to have an elite force of crime-fighters cleaning up the streets. Not to mention, I really don't want to introduce an organization into my game, either to hlep the PCs or the hinder them, that is so unilateral as to all qualify for the same PrC. Like a force of blademasters who all get baked by a single enchantment, or a mystical mage circle that can't handle poison darts. I wouldn't make a party that one-sided, why should a self-respecting organization put all its eggs in one basket too?
I guess my question is this: Do you guys use organizations to represent your PrCs? And how do you work that in your game?