You know, I was just thinking about this specifically for myself.
I'm going to try to plan out my architecture in advance, for once.
My thinking is to hold all functions in singletons, practically the whole game. And the only thing scripts on objects can do is call the singletons.
That way, moving nodes around will basically never be an issue, and I know where to find everything.
Some obvious scripts for me would be GameStateManager MenuManager IngameUIManager IngameEventManager AudioManager, and so on...
As I said, I haven't implemented this at all, but it's something I want to try.
Oh and another bonus is modularity. Scripts like AudioManager should be useful in pretty much any game.