Virtual Console. Virtual Console games are a bunch of older games for older consoles re-released to be playable on the 3DS.
(Game Boy games, Game Boy Advance games, N64 games, etc)
In the context of our forums, when we refer to VC saves, we normally mean Gen 1 or Gen 2 Pokémon games.
Yes, the 3DS can play Pokémon Red, Blue, Yellow, Green, Gold, Silver, Crystal.
And an additional tidbit: the mons can be transferred up to Generation 7 and up.
The saves of those games are have the same data structures as their retail counterpart, hence why PKHeX needs to check the save name to ensure it has the correct legality checks.