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?
Discworld...the game is hard, confusing, and sprawling, but so much enthusiasm went into the animations, voicework, and design.
Also: Gobliiins series. In a class of its own, highly inventive and sui generis French design that is often overlooked for being so oddball.