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?
The Dagger of Amon Ra was groundbreaking when it came out, but it seems to be remembered as the inferior sequel to the Colonel's Bequest. Personally, I loved the artwork, and I thought the almost-Metroidvania approach to the pre-museum bits was incredibly clever. The back half of the game was still Sierra's usual frustration-machine, but the top-tier presentation meant there was still a lot of charm to it.
I never played this sequel but I saw it's on sale for the GOG summer sale. I now know what I'll be playing this weekend.