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?
It'd be Loom as well for me. I loved Brian Moriarty's earlier game Wishbringer, and his Loom felt somewhat similar, just with graphics and music instead of a text parser. The audio tape in the box with the prologue was pretty unique as well. Sadly, the sequel Forge was never finished.