The Legend of Zelda: Link's Awakening (GB, 1993)
It's pretty amazing what Nintendo eventually managed to pull off with the original GB hardware after much simpler earlier titles. Case in point, Link's Awakening which translated the gameplay, mechanics and overall look of the SNES game near perfectly given the limitations, while also adding to the experience with stronger worldbuilding and major additions like platforming in two perspectives, as well as often more complex, distinct and tighter designed dungeons.
I also think LA has one of the most interesting settings in the Zelda series besides Majora's Mask in its fleeting island-based dream world with surreal elements like the dream fish and phone booths, and a sort of wistful and ominous tone throughout much of it. The latter really gels with how the story turns out and the limitations of the GB hardware, somehow turning them into a strength rather than a weakness.

Baldur's Gate (PC, 1998) & Tales of the Sword Coast (PC, 1999)(Expansion) - BioWare & Black Isle Studios

Super Mario Bros. 3 (NES, 1988/SNES, 1993)
SMB3 is an excellent all around package with a compelling world, great controls and great variety while also having more depth than its prequels. It's a large game that is also filled to the brim with neat stuff like the hidden warp flutes, wandering enemies on the map and secret map encounters, especially for a 1988 NES game. I don't think later 2D Mario games have topped it in terms of worldbuilding, hell the New series doesn't even come close.

Rocket Knight Adventures (MD, 1993)
RKA! This game is a smörgåsbord of all things I love about Konami during this era: fast and tight movement, great variety with a couple of shoot 'em up levels mixed in as well as a boxing duel between two giant robots, great bosses that sometimes have multiple forms or phases, great audiovisuals with some humorous touches, and near technical mastery of the system all in one package.
The jetpack, while implemented slightly better in later games, is great fun to use here as well and sometimes makes the game a contender for the fastest playing 16-bit game if you know the levels well. By the way, check out Screw Attack's Retro vs. Reboot for a laugh.

Super Mario World 2: Yoshi’s Island (SNES)
Heroes of Might and Magic III: The Restoration of Erathia/Heroes 3 (PC, 1999)

Wonder Boy III: The Dragon's Trap/Monster World II (SMS, 1989/PC, 2017)
My fave 8-bit game after SMB 3 and still one of the best MV/Platform Adventure games if we include later versions and fan remakes. Excellent presentation, the forms are distinct and fun to use, great pacing, and cool secrets like being able to switch or create platforms anywhere. There's even some non-linearity in the dungeon order if one so prefers. Last but not least this is also where the whole "beginning of the game ties into the prequel" trope comes from afaik, which was later used in Symphony of the Night.

Langrisser II (MD, 1994)
When it comes to SRPGs I think this is as good as it gets for the MD and the 16-bit gen, and the game outshines its prequel (Warsong) with its improved character customization, balancing, AI and variety. Langrisser 2 offers a very challenging game (dead characters stay dead), huge battles, cool classes like Summoner and Dragon Knight, a decent story with a lot of humour and twists, and excellent music. Still only playable in English via emulation, but you'll probably want to be able to fast forward after a few battles anyway. Also: Chou Aniki cameo.

Mother 3 (GBA, 2006)
Itoi's writing is in a league of its own and it's both more mature and better translated here than in the prequel; witty, funny, quirky and sometimes quite touching. Gameplay is also good with a fun rhythm gimmick to battles and while it's mostly linear, it works better for the story and pacing I think. The 2D pixel art and an eclectic lo-fi pop/funk/rock/orchestral mix aesthetics are timeless.

Panorama Cotton (MD, 1994)
It's pretty odd that this game even exists for the stock MD. Success, a game company that never made anything for the console prior to this (though I think some devs come from Compile), decides to turn Cotton into a Space Harrier-like shooter, make it one of the most technically impressive efforts for the system, then release a limited amount of copies exclusively for the Japanese market as late as mid-1994. Well I'm glad they did, because they certainly _succeeded_ in making Panorama Cotton an amazing game (for example you get branching paths and RPG elements years before PD Zwei here) and something of a swan song for the 2D-based rail shooter. Now if someone would port this to the MCD for super smooth scaling...

Wario Land: Super Mario Land 3 (GB, 1994)
Seirei Senshi Spriggan (PCE CD, 1991) - Sci-fi mix
The Typing of the Dead (ARC, 1999/DC/PC, 2000)
Saturn Bomberman (SAT, 1996)
Warcraft II: Tides of Darkness (PC, 1995) & Warcraft II: Beyond the Dark Portal (PC)(Expansion)
The Legend of Zelda: A Link to the Past (SNES)

Alex Kidd in Miracle World (SMS, 1986)
This takes hacks/mods into account however it's still a top 10 game without them. AK1 was an ambitious platformer for its time with an inventory system, shops, dungeon levels with switch puzzles, optional side quests and unique quirks like how you remove the ghost enemies via blocks that make it still stand out today. It's disappointing how even Sega fans in the US dismiss this one as a SMB clone when there's a lot more to it. The one thing that doesn't hold up, janken, isn't even that prominent in the game.

Donkey Kong Country (SNES)
Donkey Kong (GB, 1994)
Monster Boy and the Cursed Kingdom (PC, 2018)

Age of Empires II: The Age of Kings (PC)
Warhammer 40,000: Dawn of War & Expansions (PC) - Sci-fi w/ strong fantasy elements
Final Fantasy VII (PS1, 1997) - Mix
Mole Mania (GB, 1996)

Landstalker: The Treasures of King Nole (MD, 1992)
This game can stalk my land any time. Landstalker is... quite a bit like Zelda 3 if it was an isometric view game, but with an actually interesting story (not the usual damsel in distress and save the world thing with a silent protag), a less formulaic structure, and more challenging puzzles. The lack of a shadow when jumping and some other control quirks were only a minor annoyance for me, since I used save states hehe.

Baldur's Gate II: Shadows of Amn (PC) & Baldur's Gate II: Throne of Bhaal (PC)

Yu Yu Hakusho: Makyou Toitsusen (MD, 1994)
Was gonna put Mega Bomberman on the list but assuming we're doing PCE/TG16 (this was copy-pasted from another thread) I can mention this one instead. Growing up we used to play the 3-player fighting game International Karate+ on a buddy's Amiga a lot, and we loved the sheer chaos of it. So in the '00s when I discovered that this game had the same feature but with yet another player added, I had to play it. And (spoiler) Treasure did it once again, it's a great fighting game in the vein of Fatal Fury 2. Matches might not be as fair or precise as in Street Fighter 2 when you play like this, but the laughs from unintended results and the fun in temporary alliances make up for it.

Land of Illusion Starring Mickey Mouse (SMS, 1993)
Pocky & Rocky (SNES)
Fantasy Zone II DX (ARC/3DS) - Mix
Shining Force II (MD, 1993)
Panzer Dragoon II Zwei (SAT, 1996) - Mix
Dragon's Curse Remake (fan remake of WB3)(PC, 2008?)
Dungeon Keeper (PC)
DuckTales 2 (NES/GB, 1993)
Castlevania: Circle of the Moon (GBA, 2001)
Terranigma (SNES, 1995)
Lunar: Eternal Blue (MCD, 1994)
Virtual Boy Wario Land (VB)
Ganbare Goemon 2 (SNES)
Soul Blade/Soul Edge (PS1, 1996)
SoulCalibur (DC)
Secret of Evermore (SNES)(w/ mods)
Castlevania: Symphony of the Night (PS1)
Lords of Thunder (PCE CD, 1993/MCD, 1995)
Crystalis (NES, 1990)(w/ mods)
Lunar: Eternal Blue (MCD)
Solomon's Key (NES/ARC, 1986)
Chrono Trigger (SNES)
DuckTales 2 (NES/GB)
Castlevania: Rondo of Blood (PCE CD)
Castlevania: Bloodlines (MD)
Super Castlevania IV (SNES)
Final Fantasy Adventure/Seiken Densetsu (GB, 1991)
Ghouls 'n Ghosts (ARC, 1988/MD, 1989)
Final Fantasy V (SNES)
Gargoyle's Quest II: The Demon Darkness (NES, 1992/GB)
Gargoyle's Quest (GB, 1992/GB)
Warcraft III (PC)
Kirby's Adventure (Wii)
Kirby Super Star (SNES)
Dungeon Keeper 2 (PC)
Adventures of Lolo 1-2 (NES)
Sylvan Tale (GG)
Hamelin no Violin Hiki (SNES, 1995)
Populous: The Beginning (PC)
Solomon's Key 2/Fire & Ice (NES)
Strife (PC) - Mix