One thing that really bothered me is that the movie had Gurney Hallack warn Paul not to sit with his back to the door rather than Thufir Hawat. In the book, this was an important early scene because it's a setup for Thufir's death scene at the end, when he says, "The universe is full of doors." Of course Thufir's death hasn't been shown yet in the movies, but they already degraded it somewhat.
There were other changes that bothered me too. IIRC there was something crucial missing from the gom jabbar scene that left out a big part of the motivation for it. I don't remember all the details now. (Edit: Now I remember. The Reverend Mother explained that an animal would gnaw off its own leg to escape the trap. In the book, she explains that a human would fake death and kill the trapper to eliminate a threat to its kind. Whereas in the movie, she just says "What will you do?" WTF?!?) I stopped the movie after a half hour or so. I didn't see the point, when the book is so much better.