They are slightly less likely to scan you, and you can accept better-paying missions from the bulletin board i.e. those that used to say "this faction does not trust you enough". If the station sells either the clipper or the dropship, if you're allied with them, then you don't need the respective naval ranks. I don't know if you have to be allied instead of just friendly for this, but I read that they offer you slightly cheaper fuel as well.
If you're friendly/allied with the station because you're friendly/allied with the major faction it belongs to, then you get interdicted in SC much less often.