I'm getting back into retro gaming and I'm looking for stuff I haven't played before.

Please recommend your favorite less popular SNES, Genesis (Megadrive), or GBA games.

No need to mention widely known popular games involving:
mario, yoshi, wario
sonic
zelda
metroid
tetris
kirby
donkey kong
pokemon
final fantasy

I'm mostly interested in 2d side scrolling games, but feel free to recommend others.

Arcus Odyssey.
Wonderboy 5.

Both games are for the Sega 16 bits console.

Terranigma (SNES EU, JP only)
Devil's Crush (TG-16)
Gekibo: Gekisha Boy (TG-16)
SaGa 3 (GB)

I have great time with Comix Zone - play it on my PS VITA but Sega ported their games on many systems

ActRaiser: Basically a hybrid of a 2D platformer and an overhead view city simulator. (Too bad the sequel got rid of the simulation segments.)

Ys 3: Wanderers of Ys. Yes, this game did get a PC "remake", but the remake is so different from the original that the original is still worth playing (it's notevery game where you can get a ring that makes you invincible).

You didn't mention Castlevania; there are some nice Castlevania games for the systems you mentioned. The most obscure of these is Castlevania Bloodlines for the Sega Genesis, but there are 2 for the SNES and 3 for the GBA. (Of course, it's worth noting that the GBA games are very different from their NES counterparts.)

If you are into games like Dungeon Master, Eye of the Beholder, and Legend of Grimrock, you could check out Mazes of Fate for the GBA. There's a DS version of the game, but I believe some people who've played both prefer the GBA.

If you're willing to go back further, there are some nice NES games. There are a few obscure hybrids out there that are worth looking into:
* The Magic of Scheherazade: Hybrid of Zelda-style action and turn-based RPG combat.
* The Guardian Legend: Hybrid of a vertical scrolling SHMUP and Zelda-style actoin
* StarTropics: Hybrid of an adventure game (like a classic JRPG, but without combat) and (in dungeons) Zelda-style action. There's also a sequel called StarTropics 2.

Another good NES game is Battle of Olympus: This game could be called a Metroidvania, and it is themed after Greek mythology. That's really an 8-bit game, and I personally prefer SaGa 1, even with its strange growth mechanics and abundance of game mechanic bugs.

Yes, I'm aware, but it largely has the look and feel of a 16 bit game, and inspires the mechanics and feel of Final Fantasy Mystic Quest.

Bahamut Lagoon. Never saw a release outside of Japan, but there is a fan translation of the original SNES version.

I use to rent these 2 games a lot when I was a kid. I completed greendog but never did completed rolo. I still have the games for my megadrive
Rolo to the rescue
Greendog: The Beached Surfer Dude

https://
en.wikipedia.org/wiki/Budokan:_The_Martial_Spirit

https://youtu.be/IBCVHkrI-pc?t=10

Aero The Acro-Bat 1+2 (Genesis & SNES)
Astro Boy: Omega Factor (GBA)
Bonk's Adventure (PC Engine)
Bonk's Big Adventure (PC Engine)
Bonk's Revenge (PC Engine)
Castlevania: Rondo Of Blood (PC Engine)
Contra: Hard Corps (Genesis)
Contra III: The Alien Wars (SNES)
Decap Attack (Genesis)
Demon's Crest (SNES)
Drill Dozer (GBA)
Dynamite Headdy (Genesis)
Ghouls 'n Ghosts (Genesis)
Go! Go! Beckham! Adventures On Soccer Island (GBA)
Gunstar Heroes (Genesis)
Gunstar Super Heroes (GBA)
Klonoa: Empire Of Dreams (GBA)
Klonoa 2: Dream Champ Tournament (GBA)
Lady Sia (GBA)
The Legend Of Spyro: The Eternal Night (GBA)
Mega Man 7 (SNES)
Mega Man & Bass (SNES)
Mega Man X-X3 (SNES)
Mega Man Zero 1-4 (GBA)
Ninja Five-O (GBA)
Pop'n TwinBee: Rainbow Bell Adventures (SNES)
Ristar (Genesis)
Rocket Knight Adventures (Genesis)
Sparkster (Genesis)*
Sparkster (SNES)*
Super Bonk 1+2 (SNES)
Super Ghouls 'n Ghosts (SNES)
Vectorman 1+2 (Genesis)
Wario Land 4 (GBA)
Zero The Kamikaze Squirrel (Genesis & SNES)

*Note that the Sega Genesis Sparkster and the Super Nintendo Sparkster are different games, though they are part of the same series.

Reminds me that there's also:

Aladdin (Genesis) (I think the DOS vesion available of GOG is based off this one)
Aladdin (SNES)

Shadowrun (Genesis)
Shadowrun (SNES)

Yes, two more pairs of different games with the same title (and neither Shadowrun is like any of the PC Shadowrun games)


Another game that I saw someone speedrun:

Wiz and Liz (Genesis) (this game feels more like certain early computer games)

Then I could also mention:
Might and Magic 2 (Genesis; there's a European SNES version, but that version has critical bugs and is not recommended)
Mega Man: The Wily Wars (Genesis, contains remakes of Mega Man 1-3 and a bonus game if you beat all three of those games)
Ninja Gaiden Trilogy (SNES, remake of Ninja Gaiden 1-3)
Wizardry 1+2+3: Llylgamyn Saga (a remake of the NES games; this might be the least buggy version of Wizardry 1 out there)
Wizardry 5 (SNES)
Wizardry Gaiden 4 (SFC, game is in Japanese and can't be changed to full English without a translation patch, also this is *not* Wizardry 4)
Wizardry 6 (SFC, again game is in Japanese, but note that you could just play the DOS version (available on GOG) in English)

Also not mentioned, but some SNES RPGs:
Lufia and the Fortress of Doom (note that the intro to the game spoils the sequel)
Lufia 2: Rise of the Sinistrals (really a puzzle-RPG hybrid; there's an optional dungeon that functions as a roguelike mini-game)
Breath of Fire
Breath of Fire 2
Dragon Quest 6 (in Japanese, so needs a translation patch for English, and unfortunately the translation patch that's out there has some significant issues)
Paladin's Quest (takes place in an alien fantasy world)
Lennus 2 (sequel to Paladin's Quest, game in Japanese)
Phantasy Star 4 (OK, this is actually for the Sega Genesies, but it is good and worth playing)

Thanks.

I think I'll start with some of Barry_Woodward's suggestions:
Super Bonk (snes)
Klonoa (gba)
and the Rocket Knight / Sparkster games for the Genesis

Super Adventure Island 2.

if you don't mind imports and have a way to play them maybe Violinist of Hamelin or Do rei mi Fantasy.

Erm, those are NES games.

Also, TMNT has an early water level that is rather frustrating and must be played before you can reach the rest of the game, and there's no save system, so you have to replay that level every time you turn on the game. I think that level might be enough to ruin the game, actually.