The OpenGL shader operates on the output image and does not add any depth information, just makes the image appear to pop in or out of the display.
On Nvidia, you can use 3D Vision with a special hack/profile for Dolphin that enables 3D Vision (nvidia inspector)
On AMD, maybe you can use IZ3D (offers free red-blue mode but discontinued) or AMD 3D something. (Not very familiar, have never tried it out, don't have a decent AMD card, etc.) No clue if it works or not, or how well it performs, or glitches, etc.
On Nvidia, you can use 3D Vision with a special hack/profile for Dolphin that enables 3D Vision (nvidia inspector)
On AMD, maybe you can use IZ3D (offers free red-blue mode but discontinued) or AMD 3D something. (Not very familiar, have never tried it out, don't have a decent AMD card, etc.) No clue if it works or not, or how well it performs, or glitches, etc.