I agree that it somewhat depends on your actions...what "it" is that you have done. Say "it" is fixing a bug in the program: "I have done it in the system" means you have gone "IN" to the system to fix a bug. "I have done it on the system" means you fixed a bug USING that system. That's only one example. Like I said, you would need to be more specific with what "it" is, but even then, it might sound right either way.

Both sound ok to me. I think the choice would depend on what exactly you were doing to the software.