Are 120Hz TFTs actually sold yet? I would really like to see one close and personal. Unfortunately, I doubt they will be usable with stereo glasses - TFT latencies are simply too high for any serious stereo work (which is why we are using CRTs and polarized projectors at work).
Perceptually there is a difference, only 50Hz is correct. Not that easy to notice on normal video, but if you look at a worst case test stream like a fast white pendulum on black @50fps you will not perceive it as solid with monitor @100Hz because of the two flashes per frame.
If 100Hz actually looks worse than 50Hz, it might be one of the following issues:
1. 100Hz driving the monitor to the absolute limit, resulting in degraded output (blur, geometric imperfections).
2. The driving signal is not an exact multiple of 50Hz, resulting in judder (e.g. the monitor might be synced to 99.8Hz or 100.1Hz instead of 100Hz). This really is horrible, but can be usually fixed through custom timings.
3. Reduced flickering allows the eye to perceive imperfections in the video signal that would be otherwise hidden.
I've encountered all three issues on my CRT (Nec FE991SB). Lowering the resolution a notch and playing with custom timings usually helps.