Mario Galaxy, it literally is a perfect game in my opinion. Absolutely nothing I would change about it.

Super Metroid.
It's one of those games that I occasionally return to over the decades, the art has held up, the music is dripping with atmosphere, the gameplay mechanics are top notch, it's just a solid game.

My runner up would have to be Ocarina of time, it basically defined an entire console and it's capabilities.

I have to say Metroid Prime, Metroid prime combines a multitude of genres in one game and perfects each aspect of the genres.

I like it better than Legend of Zelda because Metroid Prime actually gives you hints if you're stuck, and the puzzles and exploration aspect aren't as difficult yet satisfying which makes the gameplay quicker than Zelda. 

While I love Mario Odyssey and 3D World just as much, those games don't really incorporate as many different gameplay mechanics that make Metroid Prime so interesting and enjoyable.

Imma be unoriginal and say Metroid Prime.

*insert long essay on why Metroid Prime is amazing and why the Wii version is the perfect use of motion controls*

Very tough question.

I'd say Super Mario Bros 3. It totally changed up the formula, expanded in huge ways and has been influential for decades to come and pushed the NES to it's limits. Super Mario World is probably the better game, but not nearly as influential, hence why SMB3 wins this one.

Would be a very hard toss up between Breath of the Wild, Smash Melee and Mario 64... and I genuinely don't think I could pick from those 3 games as they are all so different to each other in what they set out to do but all do it to utter damn near perfection.

Super Mario Galaxy.

Out of all the video games I have played, if there was one that I can actually, legitimately call "perfect", a game that I can actually give a 100%, 10/10, perfect score, it's that one.
Everything about that game just clicks. The controls, the level design, the graphics, the music, the setting, the gameplay mechanics, etc. It also helps that the best character in the entire Mario franchise makes her debut in that game. Every single time I go back to play that game I fall in love with it all over again.

I'll elaborate later but this is frankly an easy question.

LoZ OoT. This was basically my first experience with an open world type game and that alone blew me away. The other thing is that it was one of the first games that really stumped me more than a few times. I think it was the water temple mostly that I spent forever trying to get through. It was a nightmare for me, but once I accomplished it, it felt so great. I also thought the concept or being able to grow older or go back to being younger with a sword and a stone was epic. I also made sure to get the gold cartridge version. I was like a young Goldmember. lol

There are a tonne of other amazing Nin games though. It's like trying to compare steaks. Sure some are better, but they're all steaks in the end, so how bad could they really be?

Hmm good question.. BOTW would have to be up there as one of there best ever made games.
What a brain strain.