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

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.

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 or in the short term.   Soon after that, I plan a mass machine-reformatting and then a migration of the code base to C++.