I've just started a new campaign, and am most definitely using the Affliations rules. They are perfect for the knightly orders I've got in mind, and seem to be a better way to put some things (like a mage's guild from my major city) into the game without making up an entirely new prestige class. They also work quite nicely for introducing low-level PCs to the organizations that they need to be members of in order to attain some prestige classes, so you don't end up with a bunch of nobodies suddenly wanting to join an organization just because they hit 5th level.