@johne79 I've updated the wiki page for OpenTyrian with details of how to configure a game controller.
None of the ports have anything to do with RetroArch. For OpenTyrian, I would keep a keyboard plugged until you have configured your controller. It may be the case that the default setting is mapped to a button or axis that doesn't exist on your controller.
I have not looked at the other ports. I am sticking with the DOS versions for now. You can check the wiki page for the relevant port. If the info there isn't helpful, then you can visit the repos for more documentation. Links are available in the Emulator: section.
I have noticed in most ports that the game controller works fine in-game but I need a keyboard to navigate menus. My solution was to use xboxdrv to map key presses to my controller. More info below:
https://github.com/RetroPie/RetroPie-Setup/wiki/Universal-Controller-Calibration-&-Mapping-Using-xboxdrv