I like any movie that plays with concepts of reality, so Inception was onto a winner there for me
I liked the concept of being able to get into and manipulate people's dreams, that was novel enough to make it a winner for me, plus then the confusion of what is reality and what is not was icing on the cake. Reminded me somewhat of The Three Stigmata of Palmer Eldritch in theme.
District 9 I liked because it was novel again, it wasn't really what I'd been expecting from the trailer. I liked the way the aliens were very different from what we usually see, the concepts of ghetto-isation, how we might treat and react to an alien species (all a metaphor of how we treat and react to other human beings anyway.)
Donnie Darko, again the whole twist on what is real and what is not, what is in the mind and what is reality, and the whole very bizarre and surreal nature of the rabbit character had great appeal to me, and I really liked it.
Now, as for those appearing in my top ten movies of all time, probably not. Not sure Dark City would either. Eternal Sunshine I believe would get into the top 10, it was a great mix of my beloved reality-bending theme with great directing and plot. Oh and I HATE Jim Carrey, but he was awesome in this movie.
So I do have a different reaction to those movies, and would still say they were great movies (e.g. compare to Cowboys and Aliens, for example, which is a fine piece of entertainment, but in no way had any topic to discuss, thoughts to provoke, or anything of that nature.)
When it comes to art of course, greatness is always subjective
And me, I'm a sucker for "oh this is real, oh no it's not, oh yes it is, oh no look it isn't, ok this is really real this time - haha, no it isn't..."