I asked this question on Unity Answers, but they rejected it. Perhaps you fine people can provide me with some guidance! 
This is a bit of a broad question, but can any of the Unity veterans tell me a good way to organize their hierarchy? (This is not a question about empty game objects, etc.)
Examples (off the top of my head) would be:
- Everything is its own thing.
- Categorized by location (background, foreground, UI).
- Categorized by type (Players, enemies, terrain).
- etc.
So, assuming the project would grow large, what is the best way to organize this data?
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I tend to do this…
Main game transform, a root transform. It will hold all objects. Also, Unity has twice, randomly deleted a scene so I now prefab the entire scene as they do not seem to ever delete, knock on wood. I should just back up the file each day… Note to self, buy USB key.
Then, I have various items. The exact layout depends on the game, but generally I will have folders such as, camera, player, background and managers.
Then with in each, I break down the contents accordingly.
Hope that helps!
Heh…that was…confusing but thank you. And I back up my projects daily, so I should be alright on that end.