I've been working "in Linux" or "on Linux"?

Those mean different things:

• People actually improving Linux itself are working on Linux.

• People who just happen to live there to do other work are in contrast simply working in (or with or under) Linux.

So one of those is right for a given situation but wrong for the others — and vice versa.

Both are acceptable, depending on the context: as highlighted in other answers, a Linux developer updating Linux will use "on", while a Linux user will work "in" Linux. For a Linux user, I prefer "work in a Linux environment".

Google statitstics give:

• Work in Linux : 334 000
• Work on Linux : 368 000 (surprisingly high because Linux developers are a minority)
• Work with Linux : 338 000
• Work under Linux : 102 000

With Ngram viewer (thanks @Josh61 to make me discover that tool), "with" is twice more used than "in" or "on".