I noticed for about a year that my emulators (Gens, Kega Fusion, Fceux, Nestopia) etc would stutter while playing and that was incredibly annoying. It made me want to use my Android device (Moto G 2014) for emulation more than my laptop because of how smooth it was.
Then, I remembered listening to a certain Linux podcast where the host had the same issue, I believe he was using the Gnome desktop, but it applies to Cinnamon as well as they are based on the same technology. The solution is to remove the System Monitor applet if you have one. Of course, if you don't have a System Monitor applet, this won't help. My only other solution for you then, is to play your emulators in fullscreen mode. That's not ideal, though.
I like being able to monitor CPU and network usage, because "OCD", but performance is more important to me. Besides, who wants to play Sonic the Hedgehog with microstutter? Gotta go fast!