The cleanliness of your projects starts at the OS level, not inside of your NLE. Creating clean, clear, navigable folder structure is just as important as creating a clean, clear, and navigable NLE project file. If you're in the market for something to help out with this there's a couple of options (all free):
(1) Create a Template folder structure on your OS and you can simply copy/paste that folder and rename for each new project.
(2) Use Post Haste from Digital Rebellion. It's free, easy to use, customizable, and did I mention it's free.
(3) Evan Pease (@Jack_McFly) in a recent #postchat gave people to an AppleScript file that he uses. Same idea as Post Haste, but in the convient form of an AppleScript. The script is modifiable if you know how to work with AppleScript