Perhaps the best one is the Alternative Edition V2, which made these changes:
1.) MISTAKES. Many of the mistakes exclusive to the Extended Edition have been removed or corrected – such as atrocious editing, the TV censorship cuts, and the silly repeated/fabricated footage used to set up or pad scenes.
2.) COLOR CORRECTION. The 40 or so minutes of extra live footage hastily reinserted into the Extended Version by Universal/MCA was never color graded and suffers from color mismatches with the older Theatrical footage. In V.2 colour-correction has been applied to all shots, scenes and part-scenes where the mismatches are clearly apparent, which amounts to about 80% of the extra footage. However the missing “blue eyes” of the Fremen have still not been restored – a massive rotoscoping job I chose not to undertake.
3.) PROLOGUE. The painted-stills Prologue from the Extended Version has been fixed to make it a more accurate and more helpful background to the Dune universe. It has been shortened and reconfigured to avoid repetition, to avoid giving away plot points, and to correct confusing mistakes. In V.2 the Prologue has been moved to the very start of the film, before any credits and before Reverend Mother Ramallo’s introduction. In V.2 there are also slight changes to the score and the shot selection.
4.) NARRATION. The male narration from the Extended Version was chosen for this edit and most of it has been preserved, while deleting or correcting occasional voiceover mistakes or misuse by the producers. I have always found this narration to be a more persuasive than Princess Irulan’s voiceover from the Theatrical Version. In V.2 the narration has been completely removed from one scene where the Fremen watch House Atreides arrive on Arrakis.
5.) MUSIC. The Extended Version of Dune assembled my Universal/MCA is badly re-scored. It inexplicably omits Brian Eno’s ‘Prophecy Theme’ and generally the beautiful score by Toto is used far too often, too repetitively, and at times very inappropriately (eg. action music in a quiet scene). V.1 addressed this problem through restoring Eno’s music and favouring scenes and sequences from the Theatrical Version wherever possible. In V.2 the problem is further addressed by the removal or re-scoring of the music in 6 more scenes.
6.) SCENE ORDER. I have restored to their correct place a number of existing scenes that appear in the wrong part of one or both versions of the movie (eg. Duncan & Leto’s reunion, the drowned baby worm ritual that produces the Water Of Life).
7.) INTERNAL DIALOGUE. This was used successfully by Herbert in his novel but I believe it was a colossal mistake to adapt this device so literally to the screen. Many viewers including myself found much of it infuriating. In V.1 a handful of removals and edits were done to the internal dialogue, mostly in the dream sequences. In V.2. I have removed or minimized another 14 instances, again mostly without cutting any footage. Overall, the effect is a narrative that gives less away and unfolds more naturally.
8.) DELETED SCENES. Some – but not all – of the deleted scenes that appeared as an Extras feature on the 2005 Universal Region 1 DVD release have been integrated into the Alternative Edition. These are rough-looking compared to the rest of the film rest but when edited back in these scenes restore plot points, warmth and character. In V.2 I have also performed some basic color correction on these scenes but the impact is limited given the poor condition of the footage.
9.) TRANSFER QUALITY. It was noticed after the completion of V.1 that the Region 1 DVD Extended Print is actually slightly crisper that the Region 1 DVD Theatrical Print. Therefore in V.2 some Theatrical Version footage has been replaced with identical footage from the Extended print, while retaining the Theatrical Version’s superior audio source.
10.) OTHER V.2 CHANGES. Restored the destruction of the Weirding Modules; restored establishing shots in several scenes; restored several shots of Paul’s filmbook slideshow; restored and fixed one of the filmbook voiceovers and its accompanying shots.
That version seems to be the most extensive in terms of restoring the film to Lynch's vision. While some may find that to be a bad thing, I find that since most of the work has already been done, that means it'd be easier to cut without having to add as well.
Other cuts on the site aren't as extensive, but some of them managed to rotoscope some or all of the Fremen's eyes a matching blue in the scenes added in while the above didn't even try.
I'm interested in doing a cut myself, though where to begin seems overwhelming.