in a system vs. on a system

If I want to describe something within the realm/environment/domain of something), do I say in or on?

Example: Free software is common in GNU/Linux. Comment: I would like to express that free software is the most popular choice in systems running on GNU/Linux.

This can be tricky because they are used interchangeably quite a bit in related conversations. The main difference is basically ownership.

In Linux, the main shell is bash.
On Linux, the main shell is bash.

Both mean almost the same exact thing and will be used interchangeably. However "In Linux" implies that bash is a part of Linux. "On Linux" implies you can use Linux to use bash. This specific instance is more complicated because of the fact that Linux is just a kernel, and the "virtual picture" of a OS we form in our heads.

If you look at a simple example using something else:

There is a rose on the plate.
There is a rose in the plate.

The first sentence makes it seem like a rose is on top of the plate. The second makes it seem like it's part of the plate.

So applying that back to your question, does "GNU/Linux" belong as part of (or a component of) "Free Software", or is it "a part related to." Because your trying to express that "GNU/Linux" is a part of the domain of "Free Software" in seems appropriate.

I think the problem is that you're trying to avoid using a few more words in aid of being more concise, but it needs it here. Ironically, the description you give of what you're trying to say says it better, in my opinion:

Free software is the most popular choice in systems running on GNU/Linux.

If the choice is that of the user, you could reword this:

Free software is the most popular choice among those with a Linux OS.