Many of the good theories have recently been confirmed/debunked.
Dirk and Roxy living in the future was called early and oft discussed. Another big one was uu and UU being two halves of pre-scratch Sufferer, and also that the pre-scratch troll universe would be created by the B2 kids as part of a very malicious time loop. But recent events show that uu and UU really do have their own session.
We still guess that UU and uu live in the universe the kids will create though.
Oh, a big one currently being discussed: The Red Miles approaching Dirk on Earth are Jack Noir's universe-destroying attack. It's more of an assumption than a theory though, but some people believe it's just DD's attack, sent through a portal.