On the TV Tropes page for Spirit Tracks, it says this:

Whole Plot Reference: With Hyrule Historia confirming the Alternate Timelines, this game has practically the exact same storyline and progression as The Legend of Zelda: Twilight Princess.

I'm not seeing it... at all. I mean, ST reuses some things from TP, but not anything plot-relevant. But since I've recently been reading some timeline theories, it did make me wonder: what if every game was somehow parallel to a game on another timeline? What would happen if inter-timeline travel was somehow possible? There's a ton of possibilities in here, but I'm not really a fan of time-travel stories.
Before you ask, I HAVE played Explorers of X. And while I like them as a whole, I personally think that the time travel in those games makes no sense; PM me if you want to know why.

I would imagine that Twilight Princess and ALttP are parallels of each other, given how both feature shadowy parallel worlds and transformations into animals.

However, I must ponder if there is a Twilight Realm in the Downfall Timeline. (I am fairly certain, though, that found somewhere within another mirrored realm of the Downfall Timeline, there exists a giant crater, the last remnants of a world that had met with a Terrible Fate...)

Someone with loads of time and talent needs to write a fanfic tying all of the Zelda games together. I'd write it, but I keep starting fanfics for the sake of it, and I'm biased towards the Adult Timeline.

5057332 I once saw a theory (on a ZeldaWiki talk page, of all places) that the Dark Realm from Spirit Tracks was the Twilight Realm in an alternate universe, but I don't really see it. The Twilight Realm is made of black confetti, while the Dark Realm is made of the River of the Heavens (or whatever it's called) from Okami. =P
"Mirrored realm of the Downfall Timeline" = Subrosia?

I'm not usually a fan of Majora's Mask theories, but I like the idea of the World of the Ocean King being Termina.