For the most part, you can choose any names you like for the folders in your project but Unity reserves some names to indicate that the contents have a special purpose. Some of these folders have an effect on the order of script compilation. Essentially, there are four separate phases of script compilation and the phase where a script will be compiled is determined by its parent folder.
This is significant in cases where a script must refer to classes defined in other scripts. The basic rule is that anything that will be compiled in a phase after the current one cannot be referenced. Anything that is compiled in the current phase or an earlier phase is fully available.
Another situation occurs when a script written in one language must refer to a class defined in another language (say, a UnityScript file that declares variables of a class defined in a C# script). The rule here is that the class being referenced must have been compiled in a earlier phase.
The phases of compilation are as follows:-
Phase 1: Runtime scripts in folders called Standard Assets, Pro Standard Assets and Plugins.
Phase 2: Editor scripts in folders called Standard Assets/Editor, Pro Standard Assets/Editor and Plugins/Editor.
Phase 3: All other scripts that are not inside a folder called Editor.
Phase 4: All remaining scripts (ie, the ones that are inside a folder called Editor).
Additionally, any script inside a folder called WebPlayerTemplates at the top level of the Assets folder will not be compiled at all. This behaviour is slightly different from the other special folder names which also work within sub-folders (eg, Scripts/Editor works as an editor script folder but Scripts/WebPlayerTemplates does not prevent compilation).
A common example is where a UnityScript file needs to reference a class defined in a C# file. You can achieve this by placing the C# file inside a Plugins folder and the UnityScript file in a non-special folder. If you don’t do this, you will get an error saying the C# class cannot be found.