i would say Cave Story but also Phoenotopia Awakening
I was a little off-put by it at first glance, but someone here recommended it a few years ago and I gave it a try and was blown the fuck away. There is a shocking amount of thought put into the world and it just feels really good to play. I don't think the screenshots they picked on the steam page do it justice. I'm sad that it will probably never get the sequel that was planned.