Not sure if that counts, but I would say some visual novels like Steins;Gate, or the Zero Escape series. I mean that it's usually highly rated, but very niche, so underrated or even completely ignored by majority of gamers.
Other than that, the most overrated thing I can think about is the multiplayer of The Last of Us, one of the best I've played, and most people don't even know it exists.
If we talk about older series, I would say Advance Wars. It completely disappeared and too many people forgot it.