Lisa prob tops the list for me
The whole "To the Moon" series.
Fear & Hunger
If we're talking just the RPG maker series and not any of the creations, XP because pokemon essentials.
Otherwise, it's close because I love Pokemon Uranium (the game that got banned from too much success and attention IIRC) and the currently still WIP Pokemon Empire (the game where you visit the Telius region and start on a plane ride, to avoid spoilers and also it being mixed up with any other game).
I really like Pokemon Uranium mostly because of nostalgia. Saw videos of people I used to watch who didn't normally make pokemon content playing it and it's probably the first pokemon fangame I ever played and definitely the first I finished the main story of. Still waiting for post game to be released and I'm absolutely pumped for when/if it ever releases.
I love Empire it takes baseline Pokemon Reborn/Rejuvenation elements such as field effects and adds a lot to them, has 18(?/one per type) badges planned and the currently available actually feel fair while still being challenging (IMO), changes a ton of moves to make them better (splash lowering accuracy? I'll take it!), has some pretty cool fakemon (even if they're not all ones you would see in an official game design wise) with a pretty cool spinda evolution, and even changes the type chart by having normal be super effective against fairy type, making normal have an actual use. Also, you can start with a starter of just about any type, which is absolutely amazing.
Biggest problem with both, in my opinion, is that they rely on discord servers for sharing things like game dev progress/updates and such, like most every other fangame out there.
Pokémon Infinite Fusion is really good. It's Kanto but you can splice Pokémon together for fun and/or advantage, combining their types and movesets, and a ton of the possible combos have custom sprites. (The ones that don't have custom sprites use old auto-generated sprites, which are at least usually funny.)
There are about 500 canonical 'mons, which means over 200,000 fusions!
Don't trust Google, people are making fake download sites. Get the game from the Discord.
(Yes, Discord is a terrible place to keep the canonical download links. No, I don't know why it's like that. Yes, this whole thing was made in RPG Maker, somehow!)
Yume Nikki.
Like... A game made with RPG Maker or which version of RPG Maker is my favorite?
I don't think I've ever actually played anyone else's... I just made my own with RPG Maker 2 on PS2.
I loved A Blurred Line. If the guy who made it (Lysander?) appears after 20-whatever years and finally completes the story, I'd be elated. I'd even pay for it! Lol
OneShot
Fear and Hunger 2: Termina. I do love me some survival horror, dark fantasy, and the progression of time on a setting.
The Most Stupidest Game Ever - Re-duh!
Doom & Destiny (Advanced)
Orange Season was a pretty neat game when it was being made in rpg maker. When the devs changed and it got shifted into unity it turned into an awful mess.
