This might take awhile, also some depend on my mood. From best to worst.

Final Fantasy:
FFVI
FFIV
FFIX
FFXII
FFV
FFIII
FFVIII
FFVII
FFI
FFII
FFX
FFXIII

FF SIde Games
FFTactics
FFTAdvance
FF Crystal Chronicles
FFTA2
FFMQ
Crisis Core
FFX-2

Mana
Secret of Mana
Legend of Mana
Sword of Mana
Children of Mana

Dragon Quest
DQIII
DQV
DQVII
DQVIII
DQIX
DQIV
DQI
DQII

Xeno
Xenogears
Xenosaga Episode 1
Xenoblade Chronicles
Xenosaga Episode 3
Xenosaga Episode 2

Mega Man
MM2
MM7
MM4
MM8
MM9
MM3
MM5
MM1
MM6

Mega Man X
X1
X4
X2
X6
Command Missions
X5
X3
X8
X7

Persona
P3
P2 Duology
P1
P4
P4 Arena
P4 Arena Ultimax

Shin Megami Tensei
SMTIII: Nocturne
SMTIV
SMT: Strange Journey
Devil Summoner KH vs. Soulless Army
SMT1

Mario
Super Mario World
Super Mario 3
Super Mario 2
Lost Levels
Super Mario
Mario Classic
Mario Galaxy

The Legend of Zelda
Link to the Past
Twilight Princess
The Legend of Zelda
Link's Awkening
Wind Waker
Majora's Mask
Link Between Worlds
Ocarina of Time
Skyward Sword
Spirit Tracks
Phantom Hourglass
Four Sword series
The Adventures of Link

Kingdom Hearts
Chain of Memories
Birth by Sleep
358/2
Kingdom Hearts
Dream Drop Distance
Kingdom Hearts II

Castlevania
Symphony of the Night
Rondo of Blood
Castlevania
Aria of Sorrow
Circle of the Moon
Lords of Shadow
Simon's Quest

Wild Arms
WA2
WA1
WA3

Suikoden
V
II
III
I
IV
Tactics

Street Fighter
SFAlpha 3
SFII Turbo Edition
SFIII Third Strike
Super SF II Turbo
SFIV
SF1

Mortal Kombat
MK2
MK1
MK3

Guilty Gear
GGXX
GGX
GGXXAC
GGIsuka

Chrono
Trigger
Cross
Radical Dreamers

Sonic
Sonic and Knuckles
Sonic 2
Sonic CD
Sonic 3
Sonic 1

Breath of Fire
III
V
II
IV
I

Metal Gear
Snake Eater
Metal Gear Solid
Phantom Pain
Solid Snake
Sons of Liberty
Peace Walker
Guns of the Patriots
Portable OPS
Metal Gear

Silent Hill
Silent Hill 2
P.T.
Silent Hill 4: The Room
Silent Hill 3

I'll have to think of more later.