There's one canon, and then adaptations that create separate continua.

Original books by L. Frank Baum--Dorothy's adventures in Oz; Oz is real and her family eventually move there. Oz is a whimsical country where very little is serious, suspension of disbelief is the norm, and even death is unusual.

Movie adaptation: Oz is a dream or hallucination Dorothy had while in a coma. Some changes made to canon, but this is the major one.

"Wicked", bookverse: The Wicked Witch gets a name, Elphaba. Oz turns into a serious country with involved politics and religion. The Talking Animals get backstories. Dorothy is mostly off-screen and becomes an intruder rather than the center of action; in fact, she's a bit of an in-universe Mary Sue in that she acts to make major changes with little knowledge of the canon, treating it as her personal playground. (I do not believe the author means to accuse L. Frank Baum of writing Dorothy as a Sue, though; it's just a consequence of the much more serious interpretation of the actions of an innocent girl in an innocent world, transferred into a much more serious world.)

"Wicked", musicalverse: The story is based on the book, but it's a lot more upbeat and hopeful. Elphaba has major magical powers that she doesn't have in the books, and her fate is different. Dorothy is once again offscreen, and is treated like an intruder who doesn't know what she's doing.

A few more minor adaptations exist and can be considered anything from AUs of one of the other universes, good or bad parodies, or small continua in their own right.

When does a continuum split?--I would say: It splits into two continua when the new continuum is significantly different from the old continuum, and strong enough to stand on its own independent of the old.

In a way, fanfic that departs from canon too much tries to do this--the multiple canon breaks create a story that is unrecognizable from canon. But because the story is not strong enough to stand on its own, it leans on the original canon, threatening to damage it by pulling it out of shape.

I wasn't really sure on what the PPC stance on it was, so thanks for clarifying! Anyway, while it's true that Pokemon has a lot of different canons, the main traits and origins of the Pokemon are to my knowledge at least fairly consistent with on another, and this would form a serious breach of that.

Then again, I hardly think a crossover like this would be thought out well, and is indeed purely written to cash in on Pokemon's fame. I suppose it might as well be canon though; the HP movies are canon too and I'll never stop bitching about those (and in particular Deathly Hallows Part Two) either. In that sense I'm quite the hypocrite, since I'm more than willing to accept the LotR movies as canon because I can't fight myself through the books.

As for Twilight, I must admit that I own all the books and I did enjoy them somewhat, despite the characters being cardboard cutouts of Mary-Sues. (I refuse to address Edward as a Stu, because for that manliness is needed)