This just came to me so I have not had time to flesh it out, but many prestige classes required entry into an organization. They also required certain feats to be gained in order to qualify for the PrC's.
I just got the idea of entering an organization giving you special abilities due to being trained by members in higher standing. The abilities would be powerful, but they prereqs would be gained through RP, and dedication to the organization.
You get so many prestige points(not exactly a new concept) based on what you do for them. They might call on you when you need to do another quest or give you barely enough time to get both quest done. Of course you will have to convince your party to help your organization if they are not members, especially if the current quest is really important to them. You also may never be given the opportunity to get certain powers due to your organization not having anything for you or you may not think it possible to complete a quest due to timing and/or difficulty.
The basic idea is to know that if a player joins an organization they are doing it for the RP and not just because I get to be awesome at level X. The quest themselves will come, but the new abilities may not.
I would also have the organization in question give small perks similar to the ones in the Eberron book of 5 Nations.
I will probably come back to this thread in a week or so with actual ideas.