Special Folder Names in your Assets Folder
Some names for folders have special properties in Unity. Until the official docs creates a page for this information, hopefully this page will help developers.
Scripts in here are always compiled first. Scripts are output to either Assembly-CSharp-firstpass, Assembly-UnityScript-firstpass, or Assembly-Boo-firstpass. See http://docs.unity3d.com/Documentation/ScriptReference/index.Script_compilation_28Advanced29.html
Placing scripts in Standard Assets is one way for C# scripts to be able to access .js scripts or vice-versa.
Pro Standard Assets
Same with Standard Assets only files here are meant for the Pro version
The Editor folder name is a special name which allows your scripts access to the Unity Editor Scripting API. If your script uses any classes or functionality from the UnityEditor namespace, it has to be placed in a folder called Editor (can be in any subfolder).
The "Plugins" folder is where you must put any native (C/C++) dlls, which you want to be accessible by your scripts. They will also be included with your build.
Any Java .jar files you want included in your Android project, used for Java-based plugins. See http://docs.unity3d.com/Documentation/Manual/PluginsForAndroid.html
A limited, simple way to automatically add (as symbolic links) any .a, .m, .mm, .c, or .cpp files into the generated Xcode project. See http://docs.unity3d.com/Documentation/Manual/PluginsForIOS.html
If you need more control how to automatically add files to the Xcode project, you should make use of the PostprocessBuildPlayer feature. Doing so does not require you to place your files in the Plugins/iOS folder. See http://docs.unity3d.com/Documentation/Manual/BuildPlayerPipeline.html
The Resources folder is a special folder which allows you to access resources by name in your scripts, rather than by the usual (and recommended) method of direct references. For this reason, caution is advised when using it, because all items you put in the resources are included in your build (even unused assets), because Unity has no way of determining which assets may be used by your project.
The gizmos folder holds all the texture/icon assets for use with Gizmos.DrawIcon(). Texture assets placed inside this folder can be called by name, and drawn on-screen as a gizmo in the editor.
Used to replace the default web page used for web builds. Any scripts placed here will not be compiled at all.
Copied to build folder, accessable via Application.streamingAssetsPath (http://docs.unity3d.com/Documentation/ScriptReference/Application-streamingAssetsPath.html)