First, let me get this one out of the way, since there's several of them.

I remember there was a website where you could make a Pokémon however you wanted- you could make a Magikarp learn Explosion, or you could make a Spiritomb with Wonder Guard. (If only I thought of that at the time.) I used this method to hack in Pokémon I was too lazy to catch, evolve, or try to find on the GTS. I only could use the website for a few months before the internet services shut down.

From me-

These last 2 were the only shinies to make it into Y because they were the only ones with legitimate abilities and moves. (Any Pokémon with illegitimate moves or abilities couldn't be transferred up without replacing the moves and abilities.) However if I were to evolve the Electabuzz and Porygon2, their hacked abilities would change to legitimate abilities and I could replace the illegitimate moves and I could transfer them up as shiny Electivire and Porygon-Z.

From other people-
(These are mostly Pokémon sent out by twitch streamers/youtubers who have boxes of "battle ready Pokémon" that they probably cloned.)

I also had a shiny Latias from the same person, but for whatever reason it was able to transfer up, while the Latios is stuck in the limbo that is my copy of White 2. I traded the shiny Latias away.

Not sure how I got my hands on this, Victini is shiny locked in gen 5.
I also have a shiny Ditto with imposter.