Here is a list of the various standard/recommended project folders in use. These are folders which appear inside your Project window, therefore effectively within your Assets folder on your filesystem.
Unless otherwise stated these are all relevant to Unity 3.4.
|Folder name||Description||Folder location|
|Resources||Any resources you wish to load using Resources.Load must go here||Anywhere|
|Editor||Any scripts which alter the Unity editing environment itself must go in here||Anywhere, or "Standard Assets/Editor", "Pro Standard Assets/Editor", "Plugins/Editor" if in one of these special folders|
|Plugins||Any external DLLs and scripts go in here (Pro only), see: Manual: Plugins||In project root only|
|Standard Assets||Standard scripts & other assets go in here when imported (i.e. when creating a new project)||In project root only|
|Pro Standard Assets||As above but for Pro users only||In project root only|
|Gizmos||Scripts which are used to display gizmos in the editor - excluded from any build||In project root only|
|WebplayerTemplates||Scripts which are placed within this directory will not be compiled||In project root only|
|Editor Default Resources||Resources in this folder are available to EditorGUIUtility.Load(). A good place to keep GUISkins. ||In project root only|