In general; HTML, CSS and JS
; are Presentation Layer
and are used for the User Interface and interactivity.
Individual applications that are used within an Operating System
can be in written in whatever language the author chooses; as long as it can be compiled into a low-level language that is compatible with the Operating System.
And now that GNOME has Mono
as a dependency (GNOME 2.16 - Now with C#
] ) any of the CLR languages (C#, VB.Net, F#) now can be used for development
If you want to see a practical example of this; the best way to learn would be to grab the project in question and dig in.