Loom may not exactly be obscure by any standard, but I don't see it being mentioned nearly as much as, say, Day of the Tentacle or Monkey Island. But it was a truly revolutionary way of reimagining the adventure game genre, and in a very early age of point-and-click. No inventory, single mouse click interaction, using spells to interact with the environment...
Of course, you'll want to play the original floppy version to get the full story; the CD-ROM version had its dialogue heavily truncated to fit onto the CD.
What's your pick?
I think a lot of adventure game fans have heard of it but Callahan's Crosstime Saloon is pretty great and it's my favorite game designed by Josh Mandel. I really wish it could get a digital rerelease.
A lot of people really hold this one in very high regard. Unfortunately, with regards to a rerelease, the rights situation is a tangled spiderweb of immense proportions.