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I like using Checkpoint to dump saves; however, I’ve never played a custom Virtual Counsel game before, but I believe that Checkpoint should still do the trick. The last part of you post isn’t very specific so I’ll do my best to answer. No there isn’t a sticky that states which games where released. No we don’t have a sticky with all Homebrew applications made since this forum isn’t a Homebrew community/support forum. There might be a sticky that lists recommended tools to dump saves, but I’m not too certain.

Considering that gen 3 games were never released as virtual counsel games this isn’t possible since Pokémon Bank would never receive an update to connect to a game that was never a thing for the counsel. Now assuming you have the gen 3 games on your 3DS as virtual counsel games then that means your 3DS is hacked. So in that cases dump the Emerald save and the X save and use PKHeX to transfer your Emerald Pokémon to your X save. Then you can transfer them to the later gens be normal means.