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.
I actually quite like Metroid: Other M and that's almost heresy among people who like Metroid. I like all the other Metroid games too though, favorite is Zero Mission.
One I doubt any of y'all have heard of is Rex Ronan: Experimental Surgeon on the SNES. I know it sounds like I made that up, but I really liked it as a kid. It's a basic platformer with some spaceship parts where you're a tiny shrunken doctor shooting viruses and stuff with your medicine gun. The ending of the game you're in a person's brain shooting nicotine particles to cure a cigarette addiction.
I also like a lot of the 3D castlevania games, like the N64 ones and Lords of Shadow.