Well, I've only ever seen* the version included with the "Entire Mystery" blu-ray release and apparently a fresh 4K scan was done for this, with Lynch's approval. It's this very same scan that Criterion licensed for their release. Apparently it's identical, other than that they've also issued a UHD (4K) version.

Apart from this, and a couple of dubbed versions, the only alternative in the wild is (according to IMDB) an "unofficially released extended cut of the film titled 'Twin Peaks: Fire Walk With Me - The Extended Blue Rose Cut' which restores an hour of deleted footage formerly only found as bonus content on previous releases. This edition of the movie has a 196-minute runtime."

I can knock up a copy of what I have and post it somewhere you can see if you're interested in a comparison.

Edit: not true. I did watch it years and years ago, but didn't remember much when I watched my current version (which was when I put it on Plex).

The deleted footage was included on a second dvd in the Criterion pack (which we didn't watch, another day perhaps), and the wikipedia entry includes a lengthy explanation of the whys and wherefores, such as theatres not welcoming a 5-hour show runtime, and thus a lot of the humorous characters featured in the series got all cut so we could watch many long minutes of Laura Palmer & a few of her closest friends blubbering in close up. Also KM got stroppy over 'typecasting', ultimately to no avail ...

I thought the second series of Twin Peaks (despite some good bits) damaged the integrity of the first series. For me, the first series was complete, if unsatisfying. And - again, for me - FWWM compounded that damage.

My beef with mainstream-media-paid Lynch is that he opens with all the indicators of a post-modern film noir thriller, then doesn't deliver on that promise. 

According to the wikipedia, the original plan was to make three Twin Peaks films but the studio, sensing slackening public infatuation, pulled the plug. So the fault was, as usual, very much a team effort.

That's interesting. Hard to see where a third film would have fit.

I think the original plan was to capitalize (literally) on Lynch's expansive vision, but lack of prospective punters caused a hard reset.