Magneton's shiny form appeared in the Johto League, Jackson from New
Bark Town had one and used it in his battle against Ash. It was a
formiddable foe for Ash as it took down Ash's Pikachu & Cyndaquil
without even sweating. However Ash's Bulbasaur managed to take it out.
The Magneton hasnt been seen from again First Seen: Episode 270: Tie
Magikarp's shiny form appeared in Mid-Late Hoenn with a Cameo role. In
it, a trainer called Jimmy accidentally caught one while fishing.
However as soon as he did that, a trainer came along and offered to
trade it for his Charmeleon. Jimmy accepted and Magikarp was given to
the random trainer First Seen: Episode 368: The Three Animal
Appearence! The Referee School Island!!
Gyarados's shiny form appeared in late Johto, however it wasn't
officially a Shiny form. In it, Team Rocket were forcing evolutions of
Magikarp into Gyarados but the Gyarados failed to change Colour during
evolution. It got very angry and started a Rampage in the Lake of Rage
and Mahogany time. Luckily Lance Captured it and stopped it. He later
on used it in Hoenn to help stop Kyogre & Groudon's battle First Seen:
Episode 237: Talkin Bout An Evolution
Ditto's shiny form appeared in Sinnoh. When the group were on the way
to the Grand Festival, they soon discovered that something was
impersonating their Pokémon. They quickly discovered that it was two
Ditto, one of them shiny, under the control of Makina, a girl whom is
dressing up as the Elite Four Member Flint. She owns both of the Ditto
but fails to utilise strategy properly with them. The Shiny Ditto,
nicknamed Number 2 was used in a battle against Ash's Infernape as
well as Team Rocket. It has been known to transform into Piplup,
Zapdos, Staraptor, Happiny, Sudowoodo, Meowth, Wobbuffet and Croagunk.
First Seen: Episode 641: Dealing With a Fierce Double Ditto Drama!
This Pokémon was seen in early Johto. It was being researched by a
Pokémon Researcher. he tried to catch it but failed. Ash however
managed to successfully battle it with Pikachu and caught it. It
became a very important member of Ash's team and helped him win many
Gym Battles & League Matches in the Johto League. It currently spends
it's time at Oak's Lab in Pallet Town First Seen: Episode 156: Fowl
The alternate coloured Ariados appeared in Route 201 near Sandgem
Town. When Dawn visited Professor Rowan, his Piplup and Chimchar had
escaped. While looking for them, Dawn encountered a swarm of Ariados.
Managing to hold them back, she was soon rendered helpless against the
alternate coloured Ariados hiding in the trees. Using Psychic, String
Shot and Poison Sting, it managed to restrain Dawn and her Pokémon,
but eventually fell to Dawn's newly evolved Quilava which managed to
take out the entire swarm. First Seen: Dawn's New Journey
Pichu's shiny form has technically yet to appear in the animé. It
features in the recent ending based upon the Notched Ear Pichu. In
this ending, it is shown to be the rival of the Notched-Ear Pichu. No
further appearances have been slated First Seen: Get Fired Up -
Shuckle's shiny form appeared in Early-Mid Johto. In it, Old Man
Shuckle was looking for it to get the best Berry Juice's possible, a
Love Potion, aswell as the batch from the rest of his Shuckles.
However Team Rocket tried stealing it and use it for their own
uses...but rest assured it got returned to Old Man Shuckle in time
First Seen: Episode 172: A Better Pill To Swallow
Donphan's shiny form appeared in Mid-Late Hoenn. In it, it seemed that
many of the Standard Donphan were falling in love with it and were
trying to impress it with displaying their Rollout Attacks First Seen:
Episode 391: Rollout! Loving Donphan!!
The alternate coloured Dogs are one of the protectors of Crown City.
In their appearance, they appeared to try and protect Crown City from
Kodai and to attack Zoroark who was forced into doing destruction
within the city by Kodai. Though they were made with Zoroark, they
soon understood precisely what happened and helped prevent Kodai
escaping through time. First Seen: Zoroark: Master of Illusions
Dustox's shiny form appeared in Sinnoh. When the gang reach Lake
Valor, they find it is time for the Dustox Crossing. Within the Dustox
is a special Dustox owned by a trainer called Austin. This Dustox
captures the eye of Jessie's Dustox and eventually leaves its trainer
to mate with Jessie's Dustox. First Seen: Episode 541: Crossing Paths
Swellow's shiny form appeared in the Fortree Gym in Hoenn. Winona, the
Gym Leader, had one and used it in a battle against Ash. It knew
Aerial Ace and was hard to stop. It managed to take out Ash's Grovyle,
however Ash's own Swellow managed to stop it in it's tracks after a
hard long battle First Seen: Episode 361: Fortree Gym! Sky Battle!
Metagross's shiny form appeared in Sinnoh. After going their seperate
ways following another failed attempt to capture Pikachu, Jessie &
James encounter the shiny Metagross within a cave. The Metagross
quickly attacked them until they managed to make it go into a canyon.
First Seen: Episode 585: Noodles: Roamin' Off
-My old answer :P.