--Spoilers for some games below--
1. Super Mario 64
It remains my totem of precise and perfect design for platformers. A variety of gameplay elements, clarity of mechanics, rewards for exploration, charming and humorous visuals, and difficulty without being punishing. Its the full package and reminds me of that every time I replay it. (shout outs to "modern" [PS2] variants Jak and Daxter, Ratchet and Clank, and Kya: Dark Lineage)
2. The Legend of Zelda: Ocarina of Time and Majora's Mask
This one is a two-parter because both had a similar formative effect on my childhood love of games, but they have opposing tones. Ocarina of Time was the original sandbox for me, a massive world that you really felt a part of. I would spend hours walking around Kokiri Forest and Kakariko Village just taking in the environments. Majora's Mask, then, took that joy and subverted it; the familiar was there but distorted, giving me my first lesson in how manipulative--and wonderful--game design can be
3. ICO
It frustrated me at first, but the hand-holding between Ico and Yorda, I believe, is a truly beautiful thing. Its brilliant. It fosters an emotional connection like no other. And the game is just never afraid to be unique; it makes the escort quest work by making Ico invincible (meaning protecting Yorda is not an extra objective, but the only one), and fear you feel when leaving Yorda is made real by the threat of her being abducted and terrifying when she is gone and you must go forward blindly.
4. Shadow of the Colossus
Yeah, another Team Ico game (or I guess, THE other), but they are two of my all-time favorites. Shadow of the Colossus is the greatest video game story in my opinion. Wander is a tragic hero in the classic sense, a character described so minimally yet so perfectly. His arc matches the gameplay; he will do anything for this girl who he loves, even as it destroys him and perverts his being. And at the end, holding on to the stairs, being sucked into oblivion--eventually the player, and Wander, has to let go.
5. Super Crate Box
Super Crate Box taught me my most important game design lesson: unique simplicity is wonderful. Yeah, massive worlds are great, but a rewarding experience can be made just by taking classic designs and subverting them slightly. Scoring based on weapon pickups rather than enemies killed seems like an almost irrelevant detail, but it completely changes the way the game plays and makes the risk-reward element so strong. (shout outs to other indie games that consistently amaze me with their simplicity and challenge like Binding of Isaac, Spelunky, and N)
Honorable Mention: Minecraft. Because no game ever made the lack of compulsion so compelling.
Horrible Mention: Tomb Raider: Angel of Darkness. Seriously, if you want a lesson in game design, go play this game (super cheap on Steam) and note to never do anything it does. Terrible story, offensive characters, awful controls, awful combat, awful platforming, visual design that makes it impossible to separate interactive vs. non-interactive pieces of the environment, tacked on mechanics, unintuitive level design, and so many insta-kill spots that you spend more time reloading saves than playing. Animation is okay, though.