Since you're not getting any other answer here, I'll contribute what I'll warn in advance is a somewhat unsatisfactory one.
The short version is that you can't* do it. It's something that needed to be designed into the graphics engine from the ground up to be really feasible.
I looked into this very thing several years ago when the game was still alive and kicking and I was playing a lot with things like iZ3D (which you can still download and use for anaglyphic 3D if your game supports DirectX; it has the Slickriptide seal of approval).
City of Heroes isn't based on DirectX. It's OpenGL-based. There are good and bad consequences of this, but the "bad" for 3D is that there are no really functional OpenGL 3D drivers. (At least, last time I did any active searching for such.)
There's this scene in the movie _Beetlejuice_, the social worker tells the dead main-characters couple, "That's how he dies. That's how *he* (pointing at another person) dies. That's how she dies. It's all very personal." 3D in OpenGL is a lot like that. The various frame buffers and what-not (that's a technical graphics programmer term, :-p ) all have to deal with creating stereo input at a low enough level that they're effectively coupled to the game engine.
I tried several OpenGL libraries that supposedly attempted to act as general-purpose 3D "filters" and none of them worked. The only OpenGL games that supported 3D in any fashion that worked properly were games that had a 3D option built into the game as a feature.
In short - It's never going to happen because nobody is ever going to have the incentive or the source code to hack on the Cryptic Engine or whatever else in CoH it is that drives the graphics rendering functions. What you really want is something like Nvidia's 3D libraires or like iZ3D that hooks into the graphics subsystem of the computer itself. As far as I have ever been able to tell, there's no equivalent OpenGL driver that hooks into the graphics drivers on the computer. At least, none that work.
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*as with many things in the world of computer programming, the word "can't" doesn't so much equate into the concept of "impossible under any circumstances" as into the concept "so wildly impractical that nobody is likely to ever attempt it".