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.
it's interesting and ambitious for its time, but it aged poorly right from the start. It came out about 2 months after both Super Mario 64 and Crash Bandicoot, both games that nailed the formula a lot more smoothly. Although Bubsy 3D definitely laid the foundations for later 3D platformers. The art direction is kinda cute too, like a Chuck Jones era cartoon.