It's hard to not just do favorites, but that's why I think this question is so interesting. I like the idea as "games as art" as opposed to "this was the best thing ever", etc. I'm using "art" here to refer to any of the following: graphics (for the time), storytelling (likely the largest factor here), and innovative mechanics
Older Gen (atari/nes - ps2/xbox)
Super Mario World (NES)
Super Mario 64
Ocarina (N64) / (Obviously)
Sonic 3 & Knuckles (Genesis)
Pokemon (let's be serious here, it's the entire series at this point)
Baldur's Gate I, II, and Neverwinter Nights (PC)
Might and Magic 6-8, Heroes of Might and Magic III (PC)
Jade Cocoon (PS1) -
@Juggs I disagree super hard about the 2nd one, let's turn this into some kind of BS rivalry when MKX comes out.
Vagrant Story (PS1)
Final Fantasy (as a series, nitpicking just creates inane favorite disputes)
Legend of Dragoon (PS1)
Shenmue (Dreamcast)
Ikaruga (Dreamcast)
Okami (PS2)
Shadow of the Colossus (PS2)
The Elder Scrolls III: Morrowind
Newer Gen (ps3/360-present)
Journey (I cannot stress this game enough)
Brothers: A Tale of Two Sons
Limbo
Flower
Child of Light
Valiant Hearts: The Great War
The Last of Us
The King of Fighters XIII
Race the Sun
Never Alone
Portal
The Elder Scrolls V: Skyrim
Hopefully, No Man's Sky is going to be the game that redefines everything though. I have high hopes for the procedurally generated style of programming and, if it's successful, will likely change the way we not only see games, but build them.