Jurassic Park with that weird 3-d graphical tree file system and the girl geek exclaiming roughly "Cool, its Unix!" gets my vote.[1]
https://en.wikipedia.org/wiki/Fsn
There was FSV which was an open source version, and there's a newer version discussed here: http://www.phoronix.com/scan.php?page=news_item&px=MTg4MTk
EDIT:
> It's also worth bringing up a project with similar aim which was Sun's Project Looking Glass and powered by Java but that Java 3D desktop has been canned for many years now.
Holy moly this is terrifying.