The Unity***ntime is written in C/C++. This***ntime is used in any build you create using the editor - for webplayers and plugins it is installed separate from your build, whereas it is included in it for stand-alones and other platforms such as iPhone and Wii.
The editor is built on the Unity***ntime and additionally includes editor-specific C/C++ binaries.
Wrapped around the Unity core is a layer which allows for .net access to core functionality. This layer is used for user scripting and for most of the editor UI.