Top lists sorted by decade for those who just want a quick list of my personal recommendations. 
​
1980s:
Wonder Boy III: The Dragon's Trap/Monster World II/Dragon's Curse (SMS, 1989/GG/PCE)
Knightmare II: Maze of Galious/Majou Densetsu II (MSX, 1987)
Zillion (SMS, 1987)
Faxanadu (NES, 1987)
The Goonies II/Goonies 2 (NES, 1987)
Zelda II (FDS/NES, 1987)
Blaster Master (NES, 1988)
Rygar (NES, 1987)
Metroid (FDS/NES, 1986)
Spellcaster (SMS, 1988)

​Cyborg Hunter (SMS, 1988)
Tengoku Yoitoko (Welcome to Heaven)(MSX, 1987)
Zeliard (PC, 1987)
Exile (C64/AMI, 1988)?
Clash at Demonhead (NES, 1989)
Legacy of the Wizard/Dragon Slayer IV (NES, 1987)
​​Below the Root (C64/PC, 1984)
​Getsu Fuuma Den/Getsufuma Den (NES, 1987)?
Battle of Olympus (NES, 1988)
​
MV-lite/Semi-Platform Adventure/Proto-Platform Adventure:
​Ys III: Wanderers from Ys (MD/PCE CD, 1989)

Alex Kidd in Miracle World (SMS, 1986)
Kenseiden (SMS, 1988)
The Treasure of Usas (MSX)
Kid Icarus (FDS/NES, 1986)
Bionic Commando (NES, 1988)?
​
​
1990s: 
Super Metroid (SNES, 1994)
Gargoyle's Quest 2 (NES/GB, 1992)
Castlevania: Symphony of the Night (PS1, 1997)
Gargoyle's Quest (GB, 1990)​
​Wonder Boy in Monster World/Monster World III/Dynastic Hero (MD, 1991/PCE CD)
Ufouria: The Saga/Hebereke (NES, 1991)
Demon's Crest (SNES, 1994)
Monster World IV (MD, 1994)

Quackshot (MD, 1991)

DuckTales 2 (NES, 1993)​

 

Land of Illusion Starring Mickey Mouse (SMS, 1992 or 1993)

Flashback: The Quest for Identity (PC/MD, 1992)

TMNT 3: Radical Rescue (GB, 1993)
System Shock (PC, 1994)
Adventure Island IV/Takahashi Meijin no Bouken Jima IV (NES, 1994)
Dragon View/Super Drakkhen (SNES, 1994)
PowerSlave/Exhumed (SAT/PS1, 1996)
Super Adventure Island II (SNES, 1994)
Spyro 2 (PS1, 1999)​
Phantom 2040 (MD/SNES, 1995)
​

Mystical Ninja Starring Goemon (N64, 1997)​

Tails Adventures (GG, 1995)
Popful Mail (MCD, 1994)
Tomba! (PS1, 1997)
Shadow Man (N64/PC, 1999)
The Divide: Enemies Within (PS1, 1996)
Metroid II: Return of Samus (GB, 1991)
Odyssey (AMI, 1995)
Milon's Secret Castle (GB, 1993)
​Fantastic Dizzy (NES, 1991/MD, 1993)
Ax Battler (GG, 1991)?
The Adventures of Rad Gravity (NES, 1990)
Stanley: The Search for Dr. Livingston (NES, 1991)
​
Semi-PA/MV-lite:
Front Mission: Gun Hazard (SNES, 1996)
System Shock 2 (PC, 1999)
Strife (PC, 1996)
Goemon's Great Adventure/Mystical Ninja 2 (N64, 1998)
Mega Man Legends (PS1, 1997)
​Legacy of Kain: Soul Reaver (PS1/DC, 1999)
Dr. Franken II (GB, 1997)

Bionic Commando (GB, 1992)
Brave Fencer Musashi (PS1, 1998)
The Legend of Zelda: Ocarina of Time (N64, 1998)
​​​Star Wars (NES/GG, 1991/SMS, 1993)
Ghostbusters (MD, 1990)
Kirby Super Star (Great Cave Offensive mode)(SNES, 1996)
Cocoron (NES, 1991)
​G.I. Joe: The Atlantis Factor (NES, 1992)
Rayman (PS1/SAT, 1995)
The Misadventures of Tron Bonne (PS1)

Holy Umbrella: Dondera's Wild!! (SNES)
​Threads of Fate (PS1)
MediEvil (PS1)
Tomba! 2: The Evil Swine Return (PS1)
Ape Escape (PS1)
​​Alundra 2 (PS1)
​Outcast (PC)​
​​Cadash (PCE/MD/ARC)
​Unreal (PC)?
Banjo-Kazooie (N64)
Commander Keen IV (PC)?
Generations Lost (MD)
​​

2000s:
Metroid Fusion (GBA, 2002)
​Castlevania: Circle of the Moon (GBA, 2001)
Metroid: Zero Mission (GBA)
Metroid Prime (GC)
Castlevania: Aria of Sorrow (GBA)
Cave Story (PC, 2004)
Castlevania: Dawn of Sorrow (NDS, 2005)
Aquaria (PC, 2007)
Castlevania: Portrait of Ruin (NDS)
​Castlevania: Order of Ecclesia (NDS, 2008)

 

​Batman: Arkham Asylum (PC/PS3, 2009)

Metroid Prime 2: Echoes (GC)​
Shadow Complex (XBLA, 2009/Remaster, 2015)

Shaman King: Master of Spirits (GBA)

Shaman King 2 (GBA, 2005)

Mega Man ZX Advent (NDS, 2007)

Ratchet & Clank (PS2, 2002)

Wario Land 3 (GBC)

Ys: The Oath in Felghana (PC, 2005/PSP, 2010)(Ys III Remake)

Metroid Prime 3 (Wii, 2007)

Blaster Master: Blasting Again (PS1)
MegaMan ZX (NDS, 2006)

Shantae (GBC)

Banjo-Tooie (N64)
Kirby & the Amazing Mirror (GBA)

​Okami (PS2, 2006)
Castlevania: Harmony of Dissonance (GBA)
Mortal Kombat: Shaolin Monks (XB/PS2, 2005)

Scurge: Hive (DS/GBA, 2006) - Isometric

Pitfall: The Lost Expedition (Multi, 2004)

Spider-Man: Web of Shadows (NDS, 2008)

Within a Deep Forest (PC)

Kingdom Hearts (PS2, 2002)

Scooby Doo: Night of 100 Frights (PS2/GC/XB, 2002)

​LostWinds (WiiWare, 2008/iOS/PC)

Lyle in Cube Sector (PC/MD)

Nightmare Before Christmas (GBA, 2005)

An Untitled Story (PC)
​Knytt Stories (PC, 2007)

La-Mulana (PC, 2005)
Blaster Master: Enemy Below (GBC)?
Bunny Must Die (PC, 2006)

Prince of Persia: Sands of Time (GBA, 2003)

Eternal Daughter (PC)

Semi-PA/MV-lite: 
Deus Ex (PC)
​Ratchet & Clank: Going Commando/Ratchet & Clank 2 (PS2)

Legend of Zelda: Twilight Princess (GC)

Psychonauts (PC)
Beyond Good & Evil (PS2)
​​Mega Man Zero (GBA)
​Spider-Man 2 (PS2)
​The Legend of Zelda: The Wind Waker (GC)
Vampire: The Masquerade - Bloodlines (PC)
​​Mega Man Legends 2 (PS1)
​The Incredible Hulk: Ultimate Destruction (GC)
​​The Legend of Zelda: Majora's Mask (N64)
Chibi-Robo! (GC)