Something that Paradoxnt said in the suggestions thread made me think of something.
Lets say there are 3 bodies: A, B, and C(planets, asteroids, stars, whatever) in syzygy and you want to get from A to C. Will the fact that B is in between A and C cause you to have to stop at B, travel around it, then continue on to C? Or go to some third point D in order to go around B? Or can you magically travel through B in phase space? It seems to me that you should not be able to travel through B in phase space because you cannot go to phase space inside of a gravity well and in order to travel through B you would have to enter its gravity well.
As crowded as some of those solar systems seem to get it seems reasonable to imagine that an alignment like that could occur, especially considering how solar systems tend to lie on a single plane.
This also brings up the possibility of some sort of interdictor ship, like you see in Star Wars, that can be placed in between two planets and drag ships out of phase space if they happen to pass through its gravity well. This last part is pretty unlikely since I don't think you can send ships outside of a planet's gravity well without going into phase space but I'm just throwing it out there anyways.