Giant Pokémon
Giant Pokémon, while having never played a large part in terms of plot, are nonetheless a recurring theme in the Pokémon anime. There are several episodes that have a plot that revolve around unusually large Pokémon, such to the point that it seems to be a rather common mutation for Pokémon to go through.
Mystery at the Lighthouse
The concept of giant Pokémon roaming the earth was introduced by Bill, who was trying to establish contact with a giant Pokémon whose cry echoed across the ocean. Eventually, it appeared in the fog, and though it could not be seen directly due to the fog its silhouette was clearly of a giant Dragonite. However, the brief encounter ended when Team Rocket attacked the giant Pokémon and scared it off. Additionally, Gary's Krabby, compared with the one Ash recently caught, is considerably big. And when Ash's Krabby evolved to Kingler, it was considerably big.
Island of the Giant Pokémon
Although several gigantic Pokémon such as Blastoise, Charizard, and Moltres appear, they are soon revealed to be colossal robots built for a theme park.
Tentacool & Tentacruel
Just a few episodes later, this episode showed a Tentacruel large enough to knock down skyscrapers. The powerful Tentacruel even spoke to the characters through Meowth, despite Tentacruel having no psychic powers.
To Master the Onixpected
In this episode, Bruno captured a giant Onix that was three times the regular size due to there being more fertile soil in the area.
The Ancient Puzzle of Pokémopolis
The very next episode, has three giants - Alakazam, Gengar, and Jigglypuff. They are ancient Pokémon with odd markings, which were released from ancient devices that function similar to Poké Balls.
The Joy of Pokémon
A giant Magikarp appears in this episode of whom a Nurse Joy takes care of. Later in the episode, it evolves into a giant Gyarados.
The Mystery Menace
The next Giant Pokémon to show up is a Bulbasaur abandoned in the sewers. In the sewers, it grows and mutates to twice its normal size.
Bound For Trouble
Two episodes later, Ash and company land on an island that is home to giant Pidgeot and Rhydon. Tracey explained that the weather and nutritional resources on the island may have contributed to it.
Fly Me to the Moon
Ash and company were visiting an island that was inhabited by overweight Pidgey, which seemed to be brought on by bad eating habits and a general lack of exercise. However, despite this, the Pidgey were still capable of flying.
Enlighten Up!
A giant Goldeen is seen among many water Pokémon.
Now That's Flower Power!
While Roselia is normally a foot tall; the one Drew has is about the size of a small, human child.
Gulpin' it Down
The next appearance of a giant Pokémon is part-way through the Advanced Generation era, where a mysterious invention causes a wild Gulpin and Ash's Treecko to grow to the size of buildings.
Whiscash and Ash
This episode contains a story about a Giant Whiscash.
Who's Flying Now?
The Gym Leader Winona is a trainer to a larger-than-normal Skarmory.
The Garden of Eatin'
In this episode a larger than usual Snorlax appears. It is later captured by Marcel.
Claydol Big and Tall
The next Giant Pokémon is a gigantic Claydol. It nearly destroyed a small town and had to be captured inside of its own gigantic Poké Ball.
Eight Ain't Enough
Juan uses a Whiscash that seems to be the same size as the giant one in Whiscash and Ash.
Caterpie's Big Dilemma
A boy's Caterpie grows to giant size and goes on a rampage, as do Team Rocket's Pokémon. The Caterpie later evolves to Metapod, then Butterfree. Later, it goes after Team Rocket's giant Dustox.
Steamboat Willies!
The captain's Mantine seems to be bigger than normal Mantine with Dawn and Ash both being able to sit on it. The Captain also says that his Mantine is quite big in the dub.
DP107
The most prominently displayed fossil in Byron's collection is a large Claw Fossil. Were it to be revived, the Anorith would be three times larger than normal.