What's Canon?

When fiction exists only in a single medium, it's relatively easy to figure out what supersedes what. In this case, chronology is the key. However, when something moves to another area, the lines become greatly blurred, and the only way to decide what goes where is with canon.

Canon, quite simply, gives various levels of rank, which are then sorted chronologically. At the top of this pyramid lies the content creators, followed their first work and all works directly related. Below that lies other works, which may or may not be canonical.

As applied to Pokémon, this makes Nintendo/Creatures/Game Freak the top authorities, followed by Pokémon Red, Blue, and Yellow, and then Gold and Silver. The next tier consists of secondary games, such as Snap and Stadium, and The Pokémon Trading Card Game (the Game Boy TCG would lie on a sub-tier below this). The next tier contains the TV show and movies.

The area below contains all non-canonical items, such as fanfics, Kids' WB ads, as well as games with no bearing on the Pokémon world, such as Pinball and Super Smash Bros.. Most merchandise falls into here as well. You'll notice I haven't mentioned Pokémon Puzzle League. Since that is based on the TV show, it falls just below it, along with all the other TV merchandise.

Now, by no means are you required to adhere to my canon system. One could argue that all games should supersede the TV show, or vice versa. Unfortunately, Nintendo has set forth no definitive guide to Pokémon, or any other game's canon (though we can safely assume the Mario games supersede the Mario movie). In other words, don't lose any sleep.