As of March 27, 2023, the Nintendo 3DS eShop closed for business, disallowing any new purchases or downloads of software.
Main Games:
Pokemon X
Pokemon Y
Pokemon Omega Ruby
Pokemon Alpha Sapphire
Pokemon Sun
Pokemon Moon
Pokemon Ultra Sun
Pokemon Ultra Moon
Virtual Console:
Pokemon Red
Pokemon Blue
Pokemon Yellow
Pokemon Gold
Pokemon Silver
Pokemon Crystal
Side Games:
Pokemon Super Mystery Dungeon
Detective Pikachu
Pokemon Trading Card Game
Pokemon Puzzle Challenge
Pokemon Art Academy
Pokemon Battle Trozei
Pokemon Mystery Dungeon: Gates to Infinity
Pokemon Rumble Blast
Misc:
Pokedex 3D Pro
Pokemon Bank
Pokemon Dream Radar
Pokemon Transporter
Everything below is free, or are able to be bought for free but you can pay money to get added bonuses.
Free to Start:
Pokemon Rumble World
Pokemon Shuffle
Pokemon Picross
Demos:
Pokemon Omega Ruby and Alpha Sapphire Demo
Pokemon Sun and Moon Demo
Pokemon Mystery Dungeon: Gates to Infinity Demo
Detective Pikachu Special Demo
Hope this helped!