I just started with adding emus to my cab, where I use Mala and standard Mame key-bindings, so all emus need to play nice with that.
The Kega Fusion v3.64 that you listed works great with a cabinet, as it has decent command line support:
Fusion <rom> [console] [country ] [-fullscreen]
console = -sms, -gg, -gen, -md, -32x, -scd, -mcd
country = -usa -jap -eur -auto
It can also be configured to exit upon pressing the ESC key. Setting up the key-bindings was kinda annoying as binding ALT from within the GUI doesn't really work. So I had to manually edit an ini file. With Kega Fusion you have most classic Sega consoles covered.
For SNES I am currently trying out Snes9x v1.53. Some things I ran into were that it will only startup fullscreen if it was running fullscreen the last time you closed it. Also you can only exit through Alt+F4. But with Mala I can just configure Esc as a Hotkey to exit the emulator. Setting up the key-bindings was easy. I wanted to try Higan v0.93 as it is supposed to be a highly accurate emulator, but there is no documentation, and apparently no command line. There is also RetroArch v0.9.9, but it either complained about missing DLLs after I installed it, or it showed a GUI and stopped responding.
Next step for me is selecting a NES emulator.