Credit to this Reddit post by u/Aligatueur, and commenters below who added games. Went looking for some of these to play myself, figured I'd post the resource on Lemmy too.

• Pokemon Incremental: https://mangostudiosofficial.itch.io/pokemon-incremental
• Guess the Pokémon Stats: https://statle.fun/
• GPX+ (Global Pokédex Plus) : https://gpx.plus/
• PokeFarm : https://pokefarm.com/
• PokeHeroes : https://pokeheroes.com/
• PokeIdle : https://pokeidle.net/
• Pokémon Hatching Center : https://richardpaulastley.github.io/PHC/
• PokeClicker : https://www.pokeclicker.com/
• DelugeRPG : https://www.delugerpg.com/
• UnovaRPG : https://www.unovarpg.com/ Closed.
• Pokémon AutoChess : https://pokemon-auto-chess.com/
• PokeGen RPG : https://www.pokegenrpg.com/
• Pokémon Plasma : https://pokemonplasma.com/
• TPPC : https://www.tppcrpg.net/
• Eclipse RPG : https://eclipserpg.com/
• Pokémon Vortex : https://www.pokemon-vortex.com/
• Showdown : https://play.pokemonshowdown.com/
• TCGOne : https://tcgone.net/
• Pokemon TCG Simulator : https://pokemonsim.com/
• Pokémon Rise : https://pokemonrise.com/ Closed.
• PokéBox : https://pokebox.net/
• PokeExp (French only) : https://pokexp.com/
• virtuadopt : https://www.virtuadopt.com/
• Pokémon Clicker (little game) : https://www.mtchs.org/wp-uploads/StudentWork/ClickerGame/
• Poliwager : https://poliwager.net/
• The Pokemon Kingdom : https://tpkrpg.net/
• Pokerogue : https://pokerogue.net/
• PokeDoku : https://pokedoku.com/
• Pokedle : https://pokedle.com/
• Pokengine : https://pokengine.org/
• PokeNexus : https://poke-nexus.com/ (Previously Pokemon Planet)
• PikaGame : https://hackedcrusade.itch.io/pika-game
• Pokemon Creed : https://pokemoncreed.net/ (Non tested)
• Pokemon Dusk Reborn : https://pkmnreborn.com/ (Non tested)
• Pokemon Comet : https://pokemon-comet.net/