These are a few I’ve played over the years and really enjoyed. I think most are still available, but some are unfortunately only distributed via discord servers.

No particular order to these:

• Pokemon Prism - A very in-depth mod of Pokemon Crystal with 2 entirely new regions and a large catalog of Pokemon from multiple generations to capture. To my knowledge, it is a successor to Pokemon Brown
• Pokemon Brown - A very in-depth mod of Pokemon Red. This was made 2 decades ago, and was the first mod I ever played. Includes a new region and many Pokemon from different generations.
• Polished Crystal - A faithful (or not) upgrade to Pokemon Crystal.
• Pokemon Crystal Clear - A mod of Pokemon Crystal that brings in many new features and vastly upgrades the AI.
• Pokemon RedStar/BlueStar - A mod of Pokemon Red/Blue that includes the SpaceWorld 1997 assets.
• Pokemon Crystal Kaizo - A mod of Pokemon Crystal that adds in much better AI and a fair bit more difficulty. All Gen 2 Pokemon can be captured and just about every trainer presents a new level of difficulty.
• Altered Emerald - A massive mod of Pokemon Emerald that adds “(almost) every move and ability from gen 1 to 7” along with a few extras while making all 386 Gen 3 Pokemon capturable.

Edit: Just realized this wasn’t strictly Pokemon mods… Oops lol.

• Celeste Mario’s Zap & Dash (NES): SMB1 turned into a Metroidvania with Celeste mechanics ported in. I think what impresses me the most is that they got 4-directional scrolling into this engine.

• Super Metroid and A Link to the Past Crossover Randomizer (SNES): It’s an absolutely incredible technical feat that this even works. SM and ALttP smashed together into a single ROM, with a few doors that take you from one game to the other, then the item pools are shuffled together so you have to go back and forth to find one game’s items in the other. Unfortunately because ALttP is a much bigger game with a lot more items it kinda overshadows SM, you may not find this to be as replayable as the standalone randos. But I recommend trying it once because it’s just so cool the first time.

• Unfortunately I can’t find an up-to-date download link for this one, just a few Youtube videos with no link, but there’s an ongoing Panel de Pon GBC Restoration Project based on a lot of unused assets buried in the ROM before it tragically got reskinned (again, this poor IP can’t catch a break). I’ve got an older build of this on my hard drive I could upload somewhere if anyone wants it, but the version I have is far from complete.

it’s wild just how many Pokemon ROM hacks there are. there’s one that recreates Sword and Shield on the GBA and it’s pretty wild how faithful it is, it even has the raid battles. another cool one is Emerald ROWE which is an open world conversion where you can start anywhere. it uses some advanced hardware features so it doesn’t work in every emulator

there’s a hack of Sonic 3D Blast for the Saturn that basically chains all of the special stages into their own game, it’s a very cool look at what a true 3D Saturn Sonic could have been, even if the stages are all just halfpipes

if you count translations, i have poured an ungodly number of hours into Shiren the Wanderer 2 on the N64 (different from the Shiren 2 on the DS). it’s another one that doesn’t always play nice with emulators but if you take copious savestates you’ll be fine. each of the post-game dungeons is essentially a whole new game, and while i’m usually not much of a completionist i just can’t put it down

Super Mario Land DX and Super Mario Land 2 DX

There’s lot of good rom hacks to try (especially for Pomemon!) :) you might enjoy this one; it’s Pokemon Red, except all Pokemon are replaced by DBZ characters with all the ludicrousness that comes with that! Pokemon DBZ Team Training - https://www.pokemoncoders.com/dragon-ball-z-team-training/

Pokemon emerald rogue

The colorization hack looks really fun to try, thank you.

I enjoy Smash Remix for the N64 Super Smash Bros. It’s a vanilla+ experience

Digimon TCG hack of Pokemon TCG for gameboy (it’s hard)

I love all of the quality of life additions that Radical Red gave to Fire Red. Sadly, I don’t enjoy the difficulty.

I actually started playing Pokémon creepy black (GBA) the other day. it basically turns your game into the creepypasta of the same name, but also alters the dialogue here and there which leads to some funny moments.

Super Metroid VARIA Randomizer.

I have gone down the same rabbit hole lately. I’ve been playing Polished Crystal and am planning to play Modern Emerald next.

Polished Crystal adds a ton of features and I love it. They added many Pokémon that you can all catch, it adds a lot of new moves and introduces the modern types and physical/special split which I prefer. It also seems like a lot more difficult than vanilla gen 2 with revised gym leader parties. I’d suggest playing the 9bit version which has almost a decade of new features added to the 2.2.0 version you usually find.

One big favourite is the fan translation of Mother 3 for GBA.

Hands down my favorite lately is Shadowrun (SNES) - the addition of SNES Mouse support. It makes the game so, so much better. That’s been huge for me, since the game is a point-and-click adventure. It’s such a quality-of-life improvement. If the mouse existed and was common when Shadowrun was written, I have to hope that they would have thought to allow it.

Also, obviously there’s a huge community of SMW hacks, and pretty much anything well-reviewed on SMW Central, I’m liable to enjoy.

In line with yours, there’s Pokemon UItra Violet, a great hack of Fire Red for GBA. Also Pokemon Naranja, another Fire Red hack that’s based on the Orange Archipelago.