The Last of Us, Uncharted 2, Need For Speed Underground 2 as well as it's sequel Most Wanted, Burnout 3, Gran Turismo 4, and Ace Combat Zero: The Belkan War are probably what I'd consider to be close to perfect or perfect.

The Last of Us just has a great mix of survival gameplay elements and a compelling story with a high quality presentation, a mix no one had done before. Even playing it today, it doesn't feel 10 years old. Uncharted 2 feels like an action movie in a video game, it's cheesy but it's a perfect execution of the concept.

The two Need For Speed games mentioned really perfected the open world arcade racer gameplay loop, and the addition of police chases in Most Wanted was great. Gran Turismo 4 is the perfect Gran Turismo game. So many cars, so many races, great physics for the time. Burnout 3 is just the perfect tap to drift arcade racer. Great tracks, takedowns, great arcade drift handling.

Ace Combat Zero is the best Ace Combat game. The story is great, the ace squadrons are great to fight against, the entire game being an allegory for an alternate history WW2 in another universe is pulled off perfectly.