For the most compatiability and playability, use the CD-ROm version since it is tweaked and peaked for todays systems. But you have to watch a few things tho, like have proper DOS drivers for your system. If you have a pure digital joystick, chances are it wont work in DOS mode unless the joystick drivers emmulate analog in DOS mode, much like the Microsoft Sidewinder 3d Pro does, which will work analog in DOS mode. Sticks such as the MS Precision Pro with or without force feedback will not work at all!! I had to buy a replacement MS 3d pro to play these games.
RFBurns