First of all, this is my first post in this list and I would like to

Welcome.
 
While developing my application, I had to create a new binary output
file format because every standard formats I found did not fit my
needs or was expendable enough but way too heavy for this kind of use
(i.e.: GPX).

GPX with extensions is increasingly the common format.   Please be sure you *need* another format before proceeding. 

After downloading and reading the format_skeleton.c file I have of
course plenty of technical questions which come to mind :)

This is the place to ask. 
 
guess, at least for the first time, I will have to send a patch file
made against the very latest source code package of gpsbabel.

Right.
 
But if you kindly accept my patch and if it is integrated in the main
branch, how will I be able to maintain it ? Patch again ? CVS/SVN/GIT
restricted access ?

We accept patches against existing files.    Right now the tree is in CVS on Sourceforge but I plan to move it to Mercurial either on GPSBabel.org or code.google.com in the short term.   Soon after that, I plan a mass machine-reformatting and then a migration of the code base to C++.

RJL