For me it’s Yume Nikki, Cave Story and Touhou.

Yume Nikki inspired the following generation of rpg maker games and many other indie projects like Ib, Mad Father, Undertale and Omori. Cave story similarly inspired many indie developers, but both Yume Nikki and Cave Story are not that known to many players.

Touhou defined a whole genre, being the most popular bullet hell in history, but is at the same time not that popular because bullet hells is a niche genre.

In your opinion, what are other games that also have this same status?