Hmmm... Tough question, but I'll bite.
First, a reasonably intelligent plot. Yes, I know, Hollywood has to sell it to more than just Sci-Fi fans, but I would like the holes to be at least "ignoreable". Nothing out recently, with the "possible" exception of Matrix, makes that grade.
Second, I want the science to hold together. If it's a space epic, I don't want to "hear" the phaser beams or explosions. I also don't want to see space "fighters" zipping around like hyperactive mosquitos in total violation of the known rules of physics.
Finally, if it is a movie adaption of a book, I want it to FOLLOW the book as much as is practical given the difference in the two mediums.
Nothing in my memory, with the possible exception of 2001, meets those three criteria.
If you know of any others that do, by all means let me know.