Inner Space. Unlikely to work very well on a non-Windows platform because of its unique game mechanic: the icons of other programs installed on the computer are the items you’re trying to collect in this game. You’d need a Windows environment populated with other apps for it to use, or write a program that gathers the icons of the apps on your real environment and generates stub executables for the game to find.

The GPU-specific versions of MechWarrior 2. That game originally used a software renderer, but many versions of it were made for specific GPUs (this was before Direct3D and OpenGL were available), and some of them looked quite good. Some of them can be played on modern hardware because there is a shim for the GPU they were designed for (most notably the 3Dfx version), but the others cannot be played any more.