Consider POD first (for Perl), then maybe XML/XSLT. Either one will export easily to other formats.

I have a modest Perl/Tk program of some umpteen modules. In all it runs to 3629 lines of code, 1052 comment lines and a longish POD tagging along at the end. It is available on-line here...

http://starling.us/tet/gus_perl/#GUS-1

The in-line comments are for me to know which subs do what. Any snippet of Perl, however small, gets a comment if come next year I might have forgotten what it is for. The POD I usually aim at the user...or as a general overview. For the user I'll also convert the POD into HTML for display online.

Inside the link cited above cited above is a button labled "POD as HTML" which is what it says it is. But the save you the trouble of pressing it, I give same below...

http://starling.us/tet/gus_perl/gus_rpc_edit_pl/gus_rpc_edit.html

Such as it is, that is the method which works for me in writing Perl. For absolutely everything else I default to XML/XSLT. The link cited above was exported to HTML from XML/XSLT. If you like, I have something on XML/XSLT here...

http://starling.ws