Here's a couple of Pokémon who are missing from the main list of Pkmn file downloads (by which I mean http://projectpokemon.org/editing/pokesav/pokesavpkmfiles.php )
Aipom, Corsola and Taillow all hatched from eggs. Their parents were hacks, but they, themselves are legitimate.
The Raikou file is an event Pokémon. I downloaded it from the Pokésav site quite a while ago, so quite surprised it wasn't in the list *shrugs*.
More to come!