If we’re allowing Trilogy as one game then I’m going to step out a bit and go with AM2R. It’s extremely good and not “for a fan remake”, just straight up good.

If we’re talking single games made/published by Nintendo I’d go with Dread for 2D. I played through that 3-4 times back to back when it came out which was a totally new behavior for me. For 3D it’s Prime 1, still the best 3D example of the genre.