The Sega Megadrive/Genesis ones definitely use an emulator, written by M2, that has the ability to use 3d information added to the released games, but also runs 2d megadrive games normally. If you're going to try one, use Sonic 2, it has the latest version of the emulator that has much better compatibility with injected games. People with kernel access have been running these as .cia, but I don't know if anyone's tried the HANS method yet.
e: I just read the second sentence of your op again. Don't expect 3d from injected games.