Exactly that is why Nintendo and sega have realised hardly any old games in stereoscopic 3d as each game needs reprogramed to work and that takes a very long time...
I always thought that would be a really cool idea, but much easier said than done. Which is a real bummer.
There is a plugin for Snes9x for PC that does it. Runs slow as hell on my computer, which corroborates what Tomato Hentai said about it being CPU intensive.
EDIT: You should be able to get the 3D effect by crossing your eyes, if you're as into 3D as I am! It's hard but it's kinda cool. Makes you sick if you do it too long.
I wonder how the plugin decides which layers go where. Each game has a different layer mode, and like Marco pointed out, it'd take a human eye to curate which layers in which games are maybe supposed to be in the foreground even though they're background layers, etc.
Makes me think of the way Nintendo went back over the thousands of GB titles to add color palettes and screen boders for the CGB and Super Game Boy.
I know there's nowhere near a good chance of it happening, but if anyone in the forums ever wants to attempt this with an emulator, I'd be happy to sift through the tile sets of major retro games and decide which 3D layers they go on.