Well... I own Xenogears, but while it can be hard to find these days, almost everybody knows of it. I also consider it extremely overrated despite that I own it lol.
As far as truly obscure games I have the following: Dobutsu Bancho, Aura: Fate of the Ages, the first King's Field (released only in Japan), Untold Legends: Dark Kingdom, Enchanted Arms (unplayable game lol), Legend of Legaia, Samurai Champloo: Sidetracked, and lastly Ribbitking.
I'm sure I'll be told that most of these are obscure, but of my collection it's what I consider to be such.