I'll post my list of my most favorite games by system.
NES
Super Mario Bros. 3
Kirby's Adventure
Final Fantasy III
SNES
Super Mario World
Donkey Kong Country
Donkey Kong Country 2
Super Mario RPG
Final Fantasy IV/II
Final Fantasy VI/III
Chrono Trigger
Secret of Mana 2/Seiken Densetsu 3
Breath of Fire I
Breath of Fire II
Terranigma
Yoshi's Island
Final Fight 3
Kirby's Super Star
The Legend of Zelda A Link To The Past
N64
Super Mario 64
Banjo Kazooie
Banjo Tooie
Paper Mario
Bomberman Hero
The Legend of Zelda Ocarina of Time
Donkey Kong 64
Rampage Universal Tour
GCN
Super Mario Sunshine
Super Smash Bros. Melee
Sonic Adventure 2 Battle
Soul Calibur II
The Legend of Zelda Twilight Princess
Star Fox Adventures
Wii
Super Mario Galaxy
Super Mario Galaxy 2
The Legend of Zelda Skyward Sword (Aside from the motion controls which I guess I can bare with )
Super Smash Bros. Brawl
GB/GBC
Pokemon Yellow/Red/Blue/Green
Pokemon Crystal/Gold/Silver
Final Fantasy Legend III
Super Mario Land 2 Six Golden Coins
The Legend of Zelda Link's Awakening DX
GBA
Pokemon Emerald/Ruby/Sapphire
Final Fantasy I & II Dawn of Souls
Kirby's Nightmare in Dream Land
Super Mario Advance 2 Super Mario World
Super Mario Advance 3 Yoshi's Island
Super Mario Advance 4 Super Mario Bros. 3
Breath of Fire I
Breath of Fire II
Golden Sun
Advance Wars
NDS
Pokemon Black/White 1
Kingdom Hearts 358/2 Days
Mario Kart DS
Yoshi's Island DS
Kirby's Super Star Ultra
Kirby's Squeak Squad
PSX
Final Fantasy Tactics
Final Fantasy VII
Final Fantasy IX
PS2
Devil May Cry 3
Disgaea Hour of Darkness
Final Fantasy X
Final Fantasy XII
Grand Theft Auto Vice City
Grand Theft Auto San Andreas
Kingdom Hearts I
Kingdom Hearts II
Marvel VS Capcom 2
Star Ocean Till the End of Time
Tales of the Abyss
Tekken 5
WWE Smackdown VS Raw 2007
PS3
Final Fantasy XIII-2 (Amazing sequel - almost better than the original aside from the dead beat characters Serah and Caius)
PSP
Darkstalkers Chronicle Chaos Tower
Final Fantasy Dissidia
Final Fantasy Dissidia 012
Final Fantasy I Anniversary
Final Fantasy II Anniversary
Final Fantasy IV Complete Collection
Final Fantasy VII Crisis Core
Kingdom Hearts Birth By Sleep
Jeanne' D Arc
Persona 1 Portable
Persona 3 Portable
Tekken Dark Resurrection
SGEN
Streets of Rage 1
Sonic the Hedgehog
Sonic the Hedgehog 3 & Knuckles
PC
Left 4 Dead 2
Orcs Must Die! 2
Worms Armageddon
Assassin's Creed II
Counter-Strike Global Offensive
Dark Souls Prepare to Die Edition
Portal 2
Saints Row The Third
Sonic Adventure 2
Sonic CD
Ys Origin
Bioshock 1
NES
Super Mario Bros. 3
Kirby's Adventure
Final Fantasy III
SNES
Super Mario World
Donkey Kong Country
Donkey Kong Country 2
Super Mario RPG
Final Fantasy IV/II
Final Fantasy VI/III
Chrono Trigger
Secret of Mana 2/Seiken Densetsu 3
Breath of Fire I
Breath of Fire II
Terranigma
Yoshi's Island
Final Fight 3
Kirby's Super Star
The Legend of Zelda A Link To The Past
N64
Super Mario 64
Banjo Kazooie
Banjo Tooie
Paper Mario
Bomberman Hero
The Legend of Zelda Ocarina of Time
Donkey Kong 64
Rampage Universal Tour
GCN
Super Mario Sunshine
Super Smash Bros. Melee
Sonic Adventure 2 Battle
Soul Calibur II
The Legend of Zelda Twilight Princess
Star Fox Adventures
Wii
Super Mario Galaxy
Super Mario Galaxy 2
The Legend of Zelda Skyward Sword (Aside from the motion controls which I guess I can bare with )
Super Smash Bros. Brawl
GB/GBC
Pokemon Yellow/Red/Blue/Green
Pokemon Crystal/Gold/Silver
Final Fantasy Legend III
Super Mario Land 2 Six Golden Coins
The Legend of Zelda Link's Awakening DX
GBA
Pokemon Emerald/Ruby/Sapphire
Final Fantasy I & II Dawn of Souls
Kirby's Nightmare in Dream Land
Super Mario Advance 2 Super Mario World
Super Mario Advance 3 Yoshi's Island
Super Mario Advance 4 Super Mario Bros. 3
Breath of Fire I
Breath of Fire II
Golden Sun
Advance Wars
NDS
Pokemon Black/White 1
Kingdom Hearts 358/2 Days
Mario Kart DS
Yoshi's Island DS
Kirby's Super Star Ultra
Kirby's Squeak Squad
PSX
Final Fantasy Tactics
Final Fantasy VII
Final Fantasy IX
PS2
Devil May Cry 3
Disgaea Hour of Darkness
Final Fantasy X
Final Fantasy XII
Grand Theft Auto Vice City
Grand Theft Auto San Andreas
Kingdom Hearts I
Kingdom Hearts II
Marvel VS Capcom 2
Star Ocean Till the End of Time
Tales of the Abyss
Tekken 5
WWE Smackdown VS Raw 2007
PS3
Final Fantasy XIII-2 (Amazing sequel - almost better than the original aside from the dead beat characters Serah and Caius)
PSP
Darkstalkers Chronicle Chaos Tower
Final Fantasy Dissidia
Final Fantasy Dissidia 012
Final Fantasy I Anniversary
Final Fantasy II Anniversary
Final Fantasy IV Complete Collection
Final Fantasy VII Crisis Core
Kingdom Hearts Birth By Sleep
Jeanne' D Arc
Persona 1 Portable
Persona 3 Portable
Tekken Dark Resurrection
SGEN
Streets of Rage 1
Sonic the Hedgehog
Sonic the Hedgehog 3 & Knuckles
PC
Left 4 Dead 2
Orcs Must Die! 2
Worms Armageddon
Assassin's Creed II
Counter-Strike Global Offensive
Dark Souls Prepare to Die Edition
Portal 2
Saints Row The Third
Sonic Adventure 2
Sonic CD
Ys Origin
Bioshock 1