I ask this question not to request advice, but because I think it will generate interesting discussion.
I build my characters (PCs and NPCs) around story. To that end I see all classes and prestige classes, along with feats and level advancement as building blocks in the characters story. Thus if the characte rends up spending a lot of down time studying, he might gain a level as a bard or wizard, or he has a religious experience and ends of taking a level in a divine spell casting class.
With that perspective in mind - I see PrCs as little more than development of skills along a specialized line. With this perspective, the fluff around most PrCs ceases to have much relevance.
The question for discussion is if others feel the same way?
Or do PrCs really represent a specific membership or fraternity?
In my worlds orders, cabals, and secret societies, may have special abilities or prerequestites associated with them, but they are not classes. They are collections of individuals with a specific agenda.
Do others look at "Orders" in the game this way as well?
Yes, I look at organizations as being very different from PrC. And, to be honest, I prefer organizations. They can give real, in-game benefits without the whole mess created by PrCs (don't get me started on these...), and serve a much better function for getting the players interested in and interacting with the game world at large.