I got the dos games working by putting them instead in the rpix86 folder so that you could navigate to and execute them /opt/retropie/emulators/rpix86 is the default location in RetroPie v2. Sadly jazz jackrabbit doesn’t work with the emulator as far as I’m aware, but I did try Hocus Pocus and putting it in that directory, navigating into the folder and executing the .exe was all it took.

Looking at the es_system.cfg file, the dos extension appears to be .txt files, so that’s what would appear in the list of “games” in the menu. If you want to try and get the games working straight from the menu, I’d try creating a txt file with the path to the .exe and see if it runs the game kind of like a script (I have no idea how rpix86 treats txt files so this is just a guess). Another thing you could try is leaving the game folder in the roms folder, and changing the extension to .exe in es_systems.cfg. Haven’t mucked about with rpix86 to know whether either of those things work, but it’s where I’d start.