If the offset was adjustable per game, it could still be useful. There could even be a repository of conf files for games, user created. I could see the 3D community getting into this.
It's not even just a matter of adjustable offset. It's the method that you'd have to use to -get- the offset in the first place - there's a lot going on behind the scenes, and you'd have to dig into the ROM's programming to figure out what has to be done. Without having access to the source code that was used to make the ROM in the first place, you'd have to decompile the thing, work through the machine code to find what needs to be tweaked (which would require the expertise of a ROM-hacking god), and try the tweak and hope like the dickens that it doesn't make things break horribly. Somehow, you'd have to fool the game into thinking that you're a bit left (or right) of where you're actually standing. This simply isn't feasible.
Once you have that, as long as it doesn't negatively affect anything, it wouldn't be all that difficult to rig up a custom emulator that runs two sessions side-by-side, the hacked version and the regular version. But even then, you'll run into issues with the far left and far right side of the playing field hitting the 'edge' and killing your 3D as the game proceeds to stop at the same place on both screens instead of having the offset that's so necessary for the effect to work.
It's easy to make a game that uses an established 3D graphics library into proper stereoscopic 3D, such as OpenGL or Direct3D. Cobbling stereoscopy into a game that has no support for anything but 2D is difficult at best, futile at worst.