nirsoft make a tool called multimonconfig or something, you can use that to setup display presets as batchfile shortcuts and switch to them using AHK or nested batchfiles or something. I had a world of trouble until i found that one tool that lets you create the presets, nothing else would work - this was all for PPSSPP because i couldn't get it to switch into 480x272p by itself.
Can you not just set resolution in each emu, or tell retroarch what res to use? You could do that in Mednafen, surely?