I wrote that chapter in the PHB II. It was basically a combination of a system that I've been using in my games for years along with Dave Noonan's earlier work on faction/reputation (eg Five Nations). To answer your question, Azgulor, they have definitely enriched my games, and players have enjoyed them.
The one way that I use them differently than the PHB II system is that I try to have the players get the executive powers quickly. I think it's a lot more fun that way, and it's following the principle of "don't save the good stuff for last because you might never get to it." One way to accelerate the players along the road to using executive powers is to have them gain the trust of the affiliation leader. Then the affiliation leader asks the players for advice on how to use his executive powers, and, in effect, the players get to control the executive powers even though they're not high enough in aff. score yet. How could this happen? Perhaps a child has inherited a throne and needs a trusted advisor. Perhaps the thieves guild boss can't trust any of his inner circle and has to reach out to some fresh recruits just brought in that no one would expect. Perhaps the archmage is feebleminded, but his apprentice can't let anyone know or there'll be war, so she looks to the players for help.
Another tip for using affiliations to enrich the world is to have affiliations unrelated to the PCs start causing environmental effects such as plagues, wars, or holidays. I've found that adds depth to the world, introduces plot hooks, and lends a lot of verisimilitude.
Jhaelen, I'm curious. What didn't you like about the example of play from the Affiliations chapter in PHB II? I hope it wasn't the players (whose names I took from one of my gaming groups) because at least one of them is a regular poster here on ENWorld!
