Perfect Puzzle Game: Catherine

For its time, Legend of Zelda: Ocarina of Time (N64)

Recently completed: Bioshock Infinite (PC/Steam)

Current game (replaying): State of Decay (PC/Steam)

Ogre battle 64, Final Fantasy 6 and Suikoden II

I'm doing my own thing here haha. I don't like using the word perfect but oh well.

Perfect Action/Adventure Game: Uncharted 2, Shadow of the Colossus
Very different reasons for including each game, but if I could summarize my reasoning for both it would be because it is the best implementation of "being on an adventure" that I have played.

Perfect WRPG: The Witcher 3-Wild Hunt, Mass Effect 2
I really don't have any notable criticisms for this game. I could say you should have been able to have more freedom within the world, but you are playing Geralt's character and story so its an implausible criticism in this context. In fact, the only WRPG that compares IMO is Mass Effect 2.

Perfect Musical Score - Final Fantasy X

Perfect pacing/storytelling: The Last of Us
Anything in the game that had been done well can be matched by other games. Pacing and storytelling in TLOU are off the charts good however. If they weren't this good it would have been another Uncharted 3 (AKA a good game that is missing that special "oomph" that pushes it into Among Thieves territory).

Perfect Customer-Developer relationship: Rocket League and TW3
Both developers put a lot of work into their game and have formed great relationships with their consumers. With TW3 you received the physical OST and some other goodies with a physical copy, as well as 16 free DLC. Rocket League devs continually chat with the community for ideas on how to improve their game, and they are very keen on transforming those concerns into reality in a swift manner (mostly).

Perfect Military FPS: Call of Duty 4

Perfect narrative structure: Metal Gear Solid 2, Bioshock

Perfect world realization: Red Dead Redemption, Assassin's Creed 2, The Witcher 3

Perfect sim: Rollercoaster Tycoon
Perfect Rpg: Oblivion loved this back in the day.
Perfect racing: Mario kart 64
Perfect FPS: Halo 2 on link up

Tetris
Ikaruga
Vanquish

There are others I'm sure but these three at least. All of these 3 games give the player everything from the very start and still have ridiculously high skill ceiling. The player can just push the game further and further.

fps - Halo 5

tps - Gears Of War 3

Adventure - Legend Of Zelda Ocarina Of Time

Sim Racing - Forza 6

Arcade Racing - Forza Horizon 2

Fighter - Killer Instinct

Jrpg - Final Fantasy 7

RPG - Elder Scrolls 5

Rts - Age Of Empire 2

Sport - NBA 2K16

Horror/Thriller - Alan Wake

I'll add more genres later.

Metroid Prime is just perfect.

Not to me