I have a folder with shortcuts for each. And I'm still not satisfied with the input.

FSO.ahk actually is just for an On Screen Display on top of my HUD. It shows which controller mode I'm currently running.
You all know Knossos.
VoiceMacro has my voice command macros. Simple things such as "Alpha Wing, Attack my target" doing C-2-1-1, as well as a few ship control commands (like "Equalize Energy").
XPadder allows me to customize controls to a greater degree, as I use an Xbox One gamepad. I have 3 different controller modes that change the behavior of a few buttons, such as LB in Mode 1 cycles the secondary weapon bank, while LB in Mode 2 changing the secondary fire rate.
Does anyone else have crazy setups?