Having only seen two movies on this list (Avatar 'Real' and Alice in Wonderland 'Fake') my observation is hardly exhaustive, but there was a definite difference in the 3D experience.

With Avatar, the third dimension seem to come out at you from the screen - I even had a cliched duck for cover at one point. With Alice the third dimension seemed to be depth in the screen - many shots felt like you were figuratively looking down a rabbit hole, rather than being immersed within one.

And for what it's worth, I don't mind paying a few bucks extra for the 3D version, real or fake.