Giant Pokémon

Giant Pokémon, while having never played a large part in terms of plot, are nonetheless a reocurring 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.

Island of the Giant Pokémon

This episode was the earliest introduction to the concept. Although several gigantic Pokémon such as Blastoise, Charizard, and Moltres appear in gigantic forms, they are soon revealed to be humongous robots built for a theme park.

Tentacool and 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 jumbo Onix.

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 Poké Ball-esque devices.

The Mystery Menace

The next Giant Pokémon to show up is a Bulbasaur abandoned in the sewers which grows and mutates into gigantic proportions.

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.

Fortree City's Feather Carnival!

The Gym Leader Winona is a trainer to a larger-than-normal Skarmory.

Seal the Giant Nendoll!!

The last Giant Pokémon is a gigantic Claydol.

Sootopolis Gym! Juan, Artist of Water! (Part 2)!!

Juan uses a Whiscash that seems to be the same size as the giant one in Whiscash and Ash.