Depends on how you define obscure.
I've recently played Guitar Hero but for the Amiga. The most obscure video game in the world is actually the legendary puzzle game Super Gem'Z.
The story on why the game is so obscure goes as follows. During a video game event in Germany of 1992, some guy came into the event, puched the person who guarded the only RC-copy of the game that would be used to showcase it to the general public. The person then proceeded to steal the game, running away from the cops, getting away of it. After a couple of hours he then proceeded to uploaded it online. All of this happened, sans the running away from the cops and uploading it online of course, right before everyones eyes. This also includes the main programmer who
literally coded the damn game.
I couldn't confirm it but it is rumored that the guy who stole it was totally piss drunk.
After an enormous buzz regarding the situation, the publisher of the game told the single developer that he won't be compensated for the leak. The developer said "fuck it" and never released the real deal because some possibly pissdrunk retard stole the game right before everyones eyes during an important event. From what I know is that the dev never made a game again, which is a huge shame, in my opinion.
While the copy of the release candidate is still available online (there are lots of youtube videos about it), its obviously illegal. Still a fun story, though I really feel sad for the developer. Its a story that seems so unreal that it is almost an urban legend, a very german urban legend. Still, its funny as hell because its true.
From the videos and screenshots that I've seen, this game also has some faithful anime art, at least for its time. Even more impressive since the game is done by germans during the early 90s.
The other unknown games I've played aren't really obscure, only very unknown. I know about some freegames that probably only 10-15 people in the world know about. Many of these games are also really just free to download pixel art games made without a budget of regular or even just mediocre quality made for fun as a project by up-and-coming video game devs throughout the 90s and early 00s.
EDIT: If you don't believe the whole Super Gem'Z story, read the trivia
here. Also I've just realized that Chris Huelsbeck is involved with making the music for this game, which makes this obscure urban legend even funnier/sadder depending on how you see it. I only know about any of this because people told me about it way, way back. Whats funnier is that I didn't believe this story for almost a decade after I've remembered the name by accident and checked google to read up on it what feels like a long time ago.