Super Mario: Super Mario Galaxy

Zelda: Wind Waker

Metroid: Metroid Prime

Final Fantasy: Final Fantasy IX

Mega Man: Mega Man 2

Halo: Halo 3

Mario Kart: Mario Kart 8

Smash: Smash Bros Melee

Resident Evil: Resi 4

Rayman - Rayman Original
Mario - Mario Bro's 3
Panzer Dragoon - Panzer Dragoon Saga
Shining Force - Shining Force 3
Final Fantasy - Final Fantasy XII (Would love an HD version)
Grandia - Grandia 2
Resident Evil - Resident Evil 2
Street Fighter - Street Fighter 2 Turbo
Forza - Forza Horizon 2
Wipeout - Wipeout Pure
Soul Calibur - Soul Calibur 2
Disgaea - Disgaea Original
Dragon Age - Dragon Age Inquisitor
Legend of Zelda - A link to the past
Fzero - Fzero GX
Super Monkey Balls - Super Monkey Balls 2

Sonic series - Sonic 2 & Sonic CD tied

Quake series - Quake 1 & Quake 3 arena tied

Duke Nukem series - Duke Nukem 3D

Pokemon series - Red/Blue

Zelda series - A link to the past

Resident Evil series - Resident Evil 1 & Resident Evil 2 tied

Street Fighter series - Super duper Street Fighter Turbo 2 !@#$%

Megaman series - Megaman 3

Megaman series - Megaman X5

Unreal series - Unreal 1 & Unreal Tournament 1999

Castlevania series - Super Castlevania 4

Legacy of Kain series - Soul Reaver

Tekken series - Tekken 2

2D Mario series - Super Mario Bros 3

3D Mario series - Super Mario 64

Donkey Kong Country series - Donkey Kong Country 1

Silent Hill series - Silent Hill 1

Metal Gear series - Metal Gear 2: Solid Snake

Warcraft series - Warcraft 2

Onimusha series - Onimusha 2

Contra series - Contra 2

Metroid series - Metroid Prime

GTA: San Andreas
Tomb Raider Anniversary
Uncharted 2
Resident Evil 5
Far Cry 4

Uncharted 3:  Best villain, best set pieces (best single one is still the train but this had the best set), and best pacing and general story

Jak 3:  Great blend of 1's platorming and worlds along with 2's open world design with fun dune buggies and much better handled dark Jak powers as well as awesome new light Jak powers

Ratchet and Clank 3:  My favorite game of all time.  5 levels is perfect for their weapons with the big upgrade coming at level 5 (ACiT my second favorite also did this), and it was absolutely hilarious along with picture perfect platforming and my favorite MP ever

MGS 3:  In my top 5 favorite games ever.  My favorite story in any medium ever.  I cried like a baby at the end and was absolutely blown away by the twists and turns as well as the relationship between Boss and Big Boss.  Also the bosses were absolutely the best of any game ever.  They were so varied and all required entirely different playstyles and strategies and thinking on your toes to beat them.

Crash 3:  Dualshock support alone makes this one the best in the series (not counting the non-ND ones because I like to pretend they don't exist), but it also has the best level variety and bosses in the series as well as a perfect difficulty.

Spyro 1:  Just edges out Ripto's Rage for me.  The environments were great and the levels were just again just the right difficulty.  It took me 15 years to get every dragon (once I got it digitally on PS3 and there was a youtube video showing where to get on the in cloud top level that I had been missing all those years) and it has aged incredibly well just like Crash 3

Infamous 1:  Again really close race with 2 but I just like the sense of progression in 1 better.  2 did an admirable job in making you feel MORE powerful but it just couldn't replicate that feeling of going from barely lighting a bulb to flying around the city on grind rails and calling down thunderstorms

Zelda-Wind Waker (HD):  Got rid of the whacky motion controls and wasn't an early 3d clunky targeting system game.  I love them all but they all have a glaring flaw other than this one.  With the swift sail and not having to find all the maps it just feels like such a tight and fun experience without any of the usual Zelda frustration of not knowing where to go (Majora's especially suffers from this).

Mario-Galaxy 2:  I just think it has the tightest platforming and the most character of all of them.  I didn't like 3d world nearly as much and it was just a little more polished than Galaxy 1

Smash-WiiU:  More characters, more powerups, more stages, more EVERYTHING!  Also I love Charizard so I can't discount just how much I love him being his own character

Pokemon-Leaf Green:  I like green more than Red and I'm a gen wunner

Resistance 3 (by a mile):  Weapon wheel, no regen, great story, R&C style upgrading with use weapons, zany weapons, all in a modern FPS.  It takes the best parts of modern FPS gameplay and gets rid of those God awful Halo quirks like regen and 2 weapon limits which is why I love it some reviewers hated it because I guess they don't like not being able to kneel and hide to heal.

Arkham City:  Took everything I loved about the first, ironed out the creases (much smoother movement and more free flowing combat with more gadgets), and added even more to the challenges.  Also I liked the story more.

Elder Scrolls Skyrim:  Best combat, best story, DRAGONS (most well done in any game), and epic side quests

Sly Thieves in Time:  Refined Sly for the 7th gen and just made it incredibly smooth.  The time travel and relatives added some great variation

GTA 5: Smoothest gameplay and most to do without being annoyingly huge and time consuming to navigate like San Andreas.  I hated San Andreas and this is what I thought it should have been.  The one area it falls short is online but hopefully that starts to get interesting but honestly it stands on SP alone for me.

my rule almost always works with franchises. 1st the worst, second the best and third the turd.

except mass effect 3 was great and uncharted 3

God of War III
BioshocK
Mass Effect 2
Gears of War 2
LittleBigPlanet 2
Fable: TLC
Skyrim

MK : Mortal Kombat 2
Star Fox: Star Fox 64
Mario: Mario 64
Tomb Raider: Latest One
Drake: Drake 2
Mario Kart: MK8
Zelda: Skyward Sword/Ocarina of Time

The Legend of Zelda: Ocarina of Time/Wind Waker
Metroid: Super Metroid
Mario: Super Mario Sunshine/Luigi's Mansion
Smash Bros: Melee
Devil May Cry: 1
Ninja Gaiden: Sigma
Dead or Alive: 2
Bayonetta: 1
Tomb Raider: Legend
Saints Row: 2

Let me see...

Dead Rising 1

Resident Evil 5

Silent Hill 2

Metal Gear Solid 2

Halo: Combat Evolved

Uncharted 2

Final Fantasy VIII

Tales of Vesperia

The Legend of Zelda: Wind Waker

Gears of War 3

Dark Souls

Fable 2

Resistance 3

The Elder Scrolls: Oblivion

Infamous 2

Yakuza 4 (though it's the only one I've played)