I've been doing some digging, most of it unsuccessful, but I may as well start something up while I've got anything at all. I was thinking about turning this thread into an archive of content not available on DVDs (that's the key here) such as stuff that was on the now-defunct website or just never mass-produced. The more people give the more I will update this post and probably eventually the first post itself should this prove successful and turn into an archive. So far the only new thing I've discovered about the site is that there were secret codes on certain Lynch dvds, and that you could input them into a phone booth on the website for secret vids. But again, I have no clue what any of this looked like.
davidlynch.com
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Phone Booth : This was a section of the pay site that allowed the input of codes in order to watch special videos. One of these is a deleted scene from Eraserhead, introduced by Lynch himself. The code itself was from a (very) hidden extra on the Eraserhead 2000 DVD. I can't find it online, which fills me with a sadness. Apparently Darkened Room was initially only available through solving a puzzle featuring Frank Booth's Mask, but Darkened Room is now available on the Dynamic:01 DVD. If you watch Darkened Room, though, there's a code written on a piece of paper in the prologue about Bananas, which was also used to unlock yet another video, though I can't find anything about its content.
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Original Series : This was a section of the site for original series. "Rabbits" (sans episode 6) has been put on DVD as part of the Lime Green Set's Mystery Disc. "Dumbland" has been released on its own and is featured as its own disc on the Lime Green Set. 3 episodes of "Out Yonder" (which might be all of them) have been released on the Dynamic:01 DVD and the Lime Green Set's Mystery Disc. I read someone discussing this section and they also mentioned something called "Pierre and Sonny Jim", which led me to a strange video with inflated rubber gloves with Dumbland-esque faces on them.
All of the Original Series content not available on DVD:
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Rabbits Episode 3 (Rebekah) :
http://www.youtube.com/watch?v=0xLYo85DeK8
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Pierre and Sonny Jim:
http://www.youtube.com/watch?v=JY69kb64M_8
Documentaries and Other Stuff:
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Meditation Creativity Peace: This is explained and available for download (for free!) here:
http://www.curzoncinemas.com/film_on_de ... ity-peace/ & The site says it best: "The film documents David Lynch’s 16 country tour in 2007-2009 where he gave talks concerning meditation and his creative process."
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Rare Bluebob interview: This was a weird interview shown on french television, relating to the Bluebob music album with John Neff, featuring a shirtless Lynch smeared in grease and a naked woman emerging from a blue-lit cave. There's a story of how this video came to light from Neff himself in this thread, as well as a link to the video:
http://www.dugpa.com/forum/viewtopic.php?f=1&t=60
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Twin Peaks FWWM 20th Anniversary Art Exhibit: This was hosted in 2012 and is mostly self-explanatory, it was an exhibit featuring high-end fanart, essentially. Images from the artists involved are available at this site (some of the pieces, at this time, are still available for purchase):
http://www.copronason.com/tpreview2/