I'm fairly critical, so there's not too many on my list, but the biggest one is that I liked Quest 64 (somehow) when I was younger.
I also love La Mulana 1&2, along with Deadly Premonition, though those are more "cult hits" aka critical failures that 'widely disliked'. But, I'd definitely hesitate to recommend any of them to someone unless I thought they'd be into it.
This is from my childhood, but Final Fantasy: Mystic Quest for the SNES. Very simplistic compared to other titles in the series, in plot and characters and gameplay, and apparently considered to be Not Very Good. It was designed as a dumbed down game for Americans.
But the music is incredible and I have played through the game several times over the years.