1)3D looks very unnatural/surreal in games. (didn't get a chance to test in movies yet). Everything has a sort of "plastic" effect to it. Yes, the effect is quite cool, with all the depth of field and all, but the novelty factor wears off very fast, and I get this insatiable urge to stop using 3d and go back to regular view.
3D makes what you're looking at that little bit more real, it's a very hard effect to describe. The problem is that a lot of graphics are plastic-like in 2D and it's not a problem because we don't really believe the object is real because the image is 2D it helps your brain categorize that object as sort of a cartoon. This is what lends to the immersion power of 3D in games.
This was extremely pronounced on Flatout 2 for me, the cars suddenly went from feeling like regular racing cars in 2D to toy cars in 3D, they seemed more real in the sense that they were in front of me but that only highlights the flaws that they're actually pretty cartoony. It's not just me, people trying it for the first time immediately pointed out the exact same thing. Conversely games with more realistic characters such as the high detail close up models of the bad guys in Batman Arkham City cutscenes looked eerily real.
3D is a bit of a novelty but more than anything else it's main benefit is to increase immersiveness of a game, that works better with some games than others, shooting people online in CS it's just crap...but singleplayer games with atmosphere it really shines.
2)There is a very noticeable effect on the eyes and there is a form of dizziness... Not motion sickness, something else. Something very different that takes a while to wear off after every use. I cant imagine how that can possibly NOT have any health effects in the long term.
Eyestrain, a lot of active 3D systems cause this due to the flickering of the glasses, I'm not sure if you have 1st or 2nd gen Nvidia glasses but the 2nd generation I have don't cause any noticeable flicker at all, I've played for hours on end with them and been fine. To get the best experience you need the Nvidia Vision 2 kit with a Vision ready monitor, these are monitors with specific features to increase brightness of 3D and reduce flicker/eyestrain.
With my set up (specs in sig) I think 3D on my PC is actually superior to that in the cinema, I do get a bit of discomfort after a while in the cinema that I don't get at home.
3)A very large amount of people claim that 120Hz makes everything look better. General computer use, 2d and 3d games, etc. Many of these people further claim that the 120Hz has other amazing effects such as improving their performance in games because everything looks just so much better. They go as far as to say that 120Hz is better for the eyes!!! This is simply not true. I have a 25.5" 1920x1200 Asus 60Hz monitor on the wall a few inches away from the Acer and it looks just as good, and interestingly enough, JUST AS BIG.
It's likely you're misunderstanding peoples comments on 120hz, it doesn't improve image quality, it improves smoothness and responsiveness if you can run your media with a high enough frame rate to keep up. Back in the CRT days when monitors flickered higher refresh rates were easier on the eyes, LCD monitors don't suffer this issue though.
In fact the only 120hz panels are TN panels to my knowledge, which are a lot worse for image quality than PVA and IPS panels, so I don't know who's claiming that...
It is my personal opinion, but I believe its a crime to make 1080p monitors any smaller than 27 inches, and anyone who buys a smaller 1080p monitor is wasting their money.
I think a lot of people would say the opposite, 1080p @ 27" represents a very large dot pitch, the effective pixels per inch is much lower than a lot of other standard resolution/size combinations, 27" is a size much better suited for 2560x1440.