From Bulbapedia, the community-driven Pokémon encyclopedia.
Giant Pokémon, while rarely playing a large part in terms of plot, are nonetheless a recurring theme in the Pokémon anime. There are several episodes that have a plot revolving around unusually large Pokémon, such to the point that it seems to be a rather common mutation for Pokémon to go through.
List of giant Pokémon that appeared in the anime
Giant Pokémon in other media
Giant Pokémon occasionally turn up in the video games and manga series.
In Hey You, Pikachu! one of the activities involves Pikachu fishing, and it's possible to fish Pokémon much larger than average. A Fisherman on Route 222 will reward the player if he is shown a Pokémon that is larger than usual. In Pokémon Ranger: Guardian Signs, Hocus attacks the player with a giant Crobat when he is faced in the Sky Fortress.
In The Electric Tale of Pikachu, Ash catches a giant Slowpoke in Ash vs. Gary. He later gives it to Gary in exchange for his sister, May Oak.
In Pokémon Gold & Silver: The Golden Boys, a giant Sudowoodo blocks Route 36. It turns out that the Sudowoodo is giant because of dried mud covering its body.