I'm not sure if this has been discussed before. I did a quick browse through the first page and didn't see anything related.
I've been using Commander Genius v1.8.3 and have encountered a black screen upon startup of the application. Not getting to the game selection screen even. Sometimes it will exit when I press 'Enter,' other times I will have to press Alt+F4.
Last I remember, I was playing Keen 4 and I had modified the resolution settings. I used 320x200 as the game's display area and 1360x768 as the actual display resolution. Now, my monitor's native res is 1366x768.
Other miscellaneous options I changed were control configuration (with an Aftershock AP.1 PS3 controller) and there were a few others I changed that were unrelated to display.
EDIT: I've also 'installed' (via .zip extraction method) CG v1.9.5 (had to manually install libcurl.dll, libeay32.dll, and ssleay32.dll) into a separate folder and still encountered the error. From there, I searched through regedit for anything related (and readable with my personal tech knowledge) to CG, but haven't found anything that will fix it yet.
Now that I think about it, I'll take a look in %appdata%. (END EDIT)
Any help would be greatly appreciated! I'd love to get back to making my way through Keen 4-9

I got lucky and bought the 3D Realms Anthology through 3D Realms for $10 before all their wonky copyright issues came to a head.
(I love bragging about it, but no one else seems to realize how great Apogee and 3D Realms were and still are! Figured someone here might appreciate the shoutout haha)