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?
For me this would be Kings Quest 7. I just mentioned it in another post, it was the first adventure game I really liked. The Kings Quest series is often mentioned but somehow the 7th iteration gets forgotten. I think it is really quirky and fun.