This article is not meant as a set of rules which you have to follow by any means. It's more like a set of guidelines, which are meant to make your add-ons a bit more compatible to other add-ons and also make your life a bit easier when dealing with other developers.
The most important rule: Don't forget writing a manual
Even if you think using your add-on is the most trivial thing in the world - it usually isn't. A few lines about how to install and how to use it are sometimes enough, but they have to be there. Also make sure that somebody is able to read your manual. You have many (free) tools for creating good looking PDF format manuals. Use them. Don't put your documentation in Orbiter's root folder. There is a dedicated folder "doc" around for this task, but the folder "add-on docs" is also common. Don't name your manual "readme.txt". This file is often replaced soon by other add-ons.
Don't violate the copyrights of other developers
You sure don't want for this to happen to you, and in most cases in our large add-on population, you can find very well done add-ons, which just want to be credited properly in your own credits, if you use them. Does it really harm somebody to write "These meshes were done by x y z"? No!
Don't make people install your add-on before they read the important notes
Don't overwrite files from Orbiter's base distribution
It's OK to include a line about how to put a base on a planet and let the player himself figure it out how to do this. But very often such modifications damage the base orbiter installation and make it impossible to run the default scenarios. You don't need to do this, so avoid it. If you replace a file from orbiter, make sure the add-on works with all default scenarios.
Don't overwrite files from other add-ons
It's almost impossible to check the meshes or textures of all released add-ons, but often add-ons overwrite files even of popular add-ons. Like Orbiter's basic files, other add-ons may no longer function if you start overwriting their files. The same may also happen to your add-ons - do you really want to risk this trouble?
Use names and filenames that make sense
That's normally no big problem, but especially when two add-ons simulate the same historic vehicle, it may happen that both use the same parts and filenames.