I know that's not really the case. I'm merely referring to some of my experiences with PC-based RPGs where, for some odd reason, everyone in (usually) the "Good" group were working together without any faction-shattering differences. There may be some tensions between nations or subfactions, but they always seem to work together against a common enemy. My problem with that is that it assumes that everyone will band together to fight the Evil Wizard. What if the Lawful Good Merchant decides that he thinks he could profit more by not involving himself in the war, and instead waiting until later to provide goods to either side. I agree with Tesral and others when they say that the Alignment mechanic might serve a purpose in the as-is D&D game, but is ultimately flawed as it adheres to too many assumptions.
Someone else even mentioned that it is a bad idea to assume that the Evil Kingdom is the Evil Kingdom because the King is Evil. What if everyone else isn't?
Now I realize that many players and DMs like the simplicity that a black and white system provides, and I'm even willing to play with this sort of system. However, I think I prefer the Alignment thing better if it applies only to extreme circumstances. For the most part, I feel that characters should have their own motivations, and that their "alignment" is primarily based on those motivations.
Allegiances are always cool to bring into a game. Again, these should be a freeform sort of thing. The "Super Secret Council For Spying on the King's Enemies" could just as easily have psychopaths in addition to those loyal to the crown and/or humanity. Something like this seems more interesting to me, because the end result is the fact that a "Good" faction has Evil elements within it.