I used to have a link to an archive of hundreds of indie roms but it’s gone now 
RetroAchievements allows achievements for homebrew roms, so they have a list of games that people cared enough about to make an achievement set for. No links to roms but it might give you some ideas. Link
If nothing else, there’s always Disco Elysium: Game Boy Edition
I loved PSO. I played split screen on GC with my brother every day for like a couple months way back when.
I liked Sticky Business
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Aria of Sorrow is undisputably the best of the GBA titles by a significant margin. Circle of the Moon is good but it’s an early GBA title and kinda rough. Harmony of Dissonance is the worst IGAvania and you’re not missing much by skipping it.
Of the DS titles, Order of Ecclesia is my fav, though exploration is fairly limited for half the game and it’s the most challenging out of all of these imo. Also Shanoa is my fav protag of the series (and clearly the inspiration for Bloodstained’s Miriam). Portrait of Ruin is pretty close to top for me too, I think it’s a bit underrated. Dawn of Sorrow is okay, it does have some cool stuff but 1) the shoehorned touchscreen seal system is deeply unfun and by far the biggest problem, 2) the castle layout/progression is awkward and has a bad flow, and 3) going from the beautiful and unique character illustrations of Aria to the generic template anime designs of Dawn is quite jarring. But it does have my favorite bonus mode of the series so at least there’s that.
If you have access to Bloodstained, that’s quite good too. It plays like it’s Aria of Sorrow 3.
The Lord of Shadows series is its own thing, more akin to like God of War. Mirror of Fate is a metroidvania but it’s quite mediocre.
Binding of Isaac can be unfair, and while yeah that’s kinda the point and mastery can overcome most of that, some rooms are laid out in a way that it’s impossible to avoid damage. For example, a closet filled with spikes and a large troll bomb spawning and immediately homing in. This never feels good even if damage is avoided through pure luck (such as flight or explosion immunity).
Also most bosses are fine but they do love to add at least one bullshit boss per version. Rebirth brought us the dreaded Bloat, then in AB they added Hush, a bullet hellish, tanky completion mark boss that can only be attempted if reached within 30 mins or less. That wasn’t bullshit enough, so in AB+ they added Delirium, another mark boss that is hidden somewhere on the largest map in the game among 6 other bosses (which included other end bosses). Before Rep there was only 1 way to guarantee access and that was by killing Hush (2 bs bosses in a row!) Oh and the fight itself is a disorienting chaotic nightmare and honestly never fun.
I don’t think anything added in Rep compares to Delirium, though I’m never happy to see Scourge or Colostomia. Mother is difficult, but honestly getting to that fight is more annoying than the fight itself. Then Rep+ added the most devastating boss of all: barely functional online co-op that can delete your save.
Yes! It’s really incredible what they could accomplish on the GB. I wish the other two games were better.
Some that I haven’t seen mentioned yet:
Kazuko Shibuya, the artist behind these, is incredible. Pretty sure she actually made all the pixel art for FF1 (including the iconic bridge scene and UI) as I don’t think there was another pixel artist available at the time.
You might like Annihilation
I like them all so it’s tough to choose. I’ll split into mainline and spin-offs
Mainline:
Sequels/spin-offs:
I yearn for the mines
Oh yes that’s a tricky part. There’s a couple of blue magics to pick up too but that’s just more stress lol
I appreciated the maps and treasure counts too. The earlier games were especially maze-like and it saved me the hassle of a search
I’d try out an After Years sequel just to see how bad it can get but I also know I’d regret it the entire time
I, on the other hand, will not be satisfied until there’s more remakes of FF4 than mainline entries
I’m sticking with the shoto, his tatsu looks sick 
11 or 8 probably. Those are usually considered the best ones. I liked the DS remakes of 4-6 and the SFC remake of 3. I’d stay away from PS1 version of 7, though the 3DS version is a little better. I haven’t played 9 and 10 is an MMO which has a single-player only release but it’s Japan only and I never was motivated enough to mess with fan translations.
Tbh if you like any DQ, you’ll probably enjoy the others. Every game has it’s unique aspects but they’re all kinda the same game too.
Also if spin-offs are on the table, I recommend Rocket Slime and Dragon Quest Builders 2.
True though fitting the entire game into a GB rom (which maxes out at 1 mb) would be an incredible feat