>>23091591well, your rom should generate a separated save file if you save in-game and not using an emulator state
then you need something that can read that save file and extract the pokemons, each pokemon will be a individual file.pkm. Not sure what's the reader/editor for gen3, but for gen4/5 its PokeGen and for gen6 it's called PKHeX.
then you use this thing to convert them to whatever game you want to send them
then if its a direct transfer to gen6 you save your converted file.pkm to those pokemon injection QR websites, generate a QR, and do the browser trick to put it in your gen6 game
If you updated your 3ds firmware you'll need to find someone with an older 3ds version to inject and then trade them to you
