Question is nearly impossible to answer. Too many amazing games.
All time though probably along the lines of:
Metal Gear Solid 3
Gone Home
Dark Souls
Honourable mentions though.
Thirty Flights Of Loving, Animal Crossing New Leaf, Catherine, Super Meat Boy, Metal Gear Solid 4, Legend Of Zelda: The Wind Waker, Transistor, Bastion, Darkest Dungeon, Hotline Miami, Counter Strike: Source, Cave Story, Resident Evil 4, Don't Starve, Metro Last Light, Splinter Cell Chaos Theory and NEOTOKYO. I think that's most of the games that have ever contested for any of my top 3, 5 or 10.