The Exorcist III instantly springs to mind. It would be great to see a version that conforms to Blatty's original cut (prior to studio intervention), titled Legion. (Mark Kermode claims to have been shown it by Blatty on a workprint VHS.) It's one of the most underrated horror films of the last few decades, and I'd love to see it get due attention.
Serenity with all the deleted scenes, by which I don't just mean the ones on the DVDs, but the scenes/alternate takes in the workprints shown early last year. (They all turn up in the unedited script in the Visual Companion book.) I saw a test screening in London in February 2005 and even now clearly remember footage such as a more graphic shot of Mal getting stabbed by The Operative that I'd kill to see again.
And, last but not least, "Director's Cuts" of Sam Raimi's Crimewave and Darkman would be awesome too.