It's a bit less obscure these days with all of the "Hidden Gem" type videos on youtube, but the Red Star for the PS2 is still relatively unknown. I don't even remember what compelled me to play it, but I loved it. I don't play many bullet hell shooters, yet found myself weaving through bullets in this game with relative ease with a bit of practice and the beat 'em up elements were right up my alley.
The Ninja Warriors on the SNES used to be obscure, until the remake happened and now it's like every beat 'em up fan worth their salt knows about it. I'm glad to see it get the recognition now that it didn't have for many years as one of the best in the genre.
Three Dirty Dwarves on the Saturn. For years people talked about Guardian Heroes and this little masterpiece got ignored.