We have developed an application in c# .net and aim to make it deployable within our intranet. We would like to have a solid documentation to go along with it but are unsure of the best platform to document this. Any tools available to facilitate this process?
I found out about Doxygen, Htmlhelp or Dr Explain but i'm still not convinced what to use.
If want to generate something similar to MSDN, you could try Sandcastle (which is created by Microsoft).
You can either use the Help File Builder for users or Documentation Compiler for Managed Class Libraries if your application is a shared library for other developers (although from your description it sounds like you will want to use the Help File Builder).
If you want MSDN-like code documentation, you can also try VSdocman.