There are areas where 3D Vision clashes with techniques employed by certain engines. The good news about 3D Vision is that it supports most games out of the box, and I've yet to find a 3D game or app where 3D Vision point-blank doesn't work. That said, in some games it just doesn't work that successfully. nVidia itself rates games as excellent, good, fair or poor (you can find the current list here) and when you start up a game a handy message will appear to inform you of any options or detail settings you should probably switch off. The biggest offender is probably Crysis, where you'll have to switch down several detail settings and prepare for some weird anomalies during play that, effectively, make it not worth the bother.
I also saw some odd behaviour with the distant backgrounds in FEAR 2, while Sony's new free MMO, Free Realms, was an almost total disaster, with ghosting all over the place. I'm sure that, should 3D Vision take off, developers will start looking at their games with reducing these anomalies in mind. In fact, some of the issues with on-screen furniture will disappear anyway, as developers further distance their games from such distractions (just as Bioshock, Mirror's Edge, Killzone 2 and Prince of Persia have already done).
Let's not be silly about this. Given that you'll either need a new monitor and £129 or £400 to use it, 3D Vision is currently a luxury item for the high-end PC gamer; the equivalent of a new top-of-the-range graphics card or a brand new gaming console. Game support is good and getting better, and the glasses don't have any major drawbacks in terms of comfort or battery life (estimated at 40 hours). All the same, the success of the effect varies from game to game, and not all users will get the most out of the system.
That's all very sensible and perfectly true. All the same, when the effect does work it's a knockout, and if I had to choose at the moment between spending £400 on a new graphics card for a few more FPS and a higher detail setting in Crysis or spending £400 on 3D Vision, I know which way I'd lean. This isn't a perfect product yet, but it's one that's aiming straight in the right direction, and with cost reductions and increased availability of 120Hz capable monitors - preferably new ones with a 1080p or higher resolution - it might just get there. Right now I'd recommend you try it, because once you do you won't look at 2D gaming in quite the same way ever again.
nVidia 3D vision is the best designed and most considered 3D gaming system yet, with decent out-of-the-box software support and an adjustable, comfortable setup. If you're serious about PC games, you owe it to yourself to try it.