The Ys games. Sure they're a bit more well known now, but I still consider them obscure, at least in North America. Also I remember I have a game called Away: Shuffle Dungeon (bet nobody here heard of it) that I remember being quite good.
"Ow! Stop! Despite my name, I AM NOT A TORCH!" -Masontorch, Ys I & II Chronicles
It seems like this topic or an analog comes up all the time, and I get tired of answering the same thing, so I'll just throw something out that isn't really my favorite game, but made an impression none the less.
Analogue: A Hate Story (analog...analogue, see what I did there?) is digital novel that is relatively heavy on novel and light on pictures, but it is structured well enough to be entertaining in its own right, so I can forgive the limited fan-service.
The twist, however, is what the game is really about, and it is rather horrifying. More so when you think that it can happen, it did happen, it does happen. Too bad the message would go right over the heads of the people who need it the most.
I am a well-known troll. Please don't fall for my shenanigans.