I prefer the two Scifi minis to the Lynch movie. I suppose an argument could be made for the style of the Lynch movie, but in terms of telling the story
, the 2000 Scifi mini is certainly better. In most cases I prefer its casting as well.
I haven't read any of the non-Herbert books myself, but of those I will say that the first four (through God Emperor) are certainly the best. Both Heretics of Dune and Chapterhouse: Dune had me falling into a pattern of not being able to manage more than one chapter at a time for most of the book, and then suddenly becoming awesome in the last quarter of the story.