A week ago I was CC'd in on a thread about Linux packaging, and how to avoid doing it the wrong way (i.e. RPM, Deb, etc.). I've always used MojoSetup and I've never forced distributions to do any additional work, but this is still a new concept to a lot of people. Additionally, Amos suggested that I expand on Itch's FNA appendix, so here's a guide on how I package my games.
This is a bit of an expansion on my MAGFest 2016 presentation, which you can find here:
I would recommend looking at that first! After that, read on...