I was thinking about a feature, but now that I think about it, I am not sure a lot of people would use it. For some games, you have to wait sometimes, and so I was trying to use another program while Jnes was running, but it would pause the game. (For example, in Final Fantasy, I would tell all the guys to attack and then want to send an IM to someone while the battle was going on). I was wondering if there was a way so that the game would not pause when I was using another application. Now that I think about it, this may be very annoying for some games if you accidentally click outside the Jnes window.
I am not sure if a lot of people would use it, but just an idea.