It is almost always necessary to change your graphics settings for modern games in order to play. Generally you want to turn off any full-screen effect, like "anti-aliasing" or "bloom".
I am a big fan of World of Warcraft, so I was so happy when I got WoW to work on my 3D monitor. I also tested the operation on anaglyph glasses -- the effect also worked well, however there was somewhat more ghosting, and the colors were affected by the color of the glasses. Still, playing WoW this way is unbelievable, it radically increases the immersiveness of the world. Sadly there is no simple way I can see to get a screenshot, or I would post it to this site (I might try and get a digital photo of it to show).
Here is a list of games I've tested that work well (and I will update as I try more):
World of Warcraft (turn off blooming and anti-aliasing)
Titan Quest (very minor problems with offset HUD elements)
Fate
Dungeon Siege (very minor problem with cursor)
Asheron's Call
You will notice that the games in this list are all really excellent games!
Here is a list of games that work, but may have some minor problems:
Evil Genius (terrain polygons drop out at edges occasionally)
Here is a list of games that don't work or don't work well enough to play:
The Elder Scrolls: Oblivion (cannot get 3D to converge correctly)
Second Life (text is unreadable)
Sims 2 (no 3D in world)
Warcraft III (no 3D in world)
The Elder Scrolls IV: Oblivion (text unreadable, white bars on edges)
Matrix Online (models detach in weird ways)
The Longest Journey
There are various websites that list games that work, however I've found the lists to be out-of-date and misleading. For example Warcraft III may work in stereo 3D, but the play area is in 2D -- basically you get two layers, one for the user interface elements and one for the play area. It may work, but is not worth it.
The Future of Stereo 3D Games
Sadly the future of these games is not all that bright; the simple reason is that improvements in hardware and software technology now require the use of "render-to-texture" technique. A "texture" is a 2D image used to paint a 3D model; render-to-texture means that instead of rendering the 3D scene to your video card's output buffer, the scene is rendered to a 2D texture first. This is done so that various "post-processing" effects can be done, just as post-processing effects are done to film movies. These effects may consist of blooming, anti-aliasing, high-dynamic range processing or changing the overall tone.
Turning off these effects may not guarantee your game will work, also some of these effect may be out of your control. Unless a game is specifically designed for Stereo 3D, it is pure luck that it can be configured to work, and as these games advance, the likelihood of working is reduced. Furthermore video game consoles would need specific software to output field sequential frames.
No improvement in favor of Stereo 3D is likely for PC or video games in the foreseeable future -- expect to see fewer and fewer compatible games. The percentage market for stereo 3D is very small, making the extra effort required to support this not worthwhile.
The only possibility that James Cameron and George Lucas release their big titles in 3D for movies. This might having the effect of making 3D cinema at home more popular, which might increase demand for 3D games. This is a lot of "mights".