Warning: Major spoilers ahead.
1. Adam is actually Bartosz and not Jonas.
In the course of the series, the horrifically scarred Adam reveals himself to be an old Jonas. However, a major theory that several people on Reddit have been getting behind is that Adam is actually Bartosz.
The theory opines that Bartosz is actually manipulating Jonas by pretending to be him, which is quite probable because we never see Bartosz in any other timeline. Also, considering he's in love with Martha and resents Jonas, he also has the motivation to ruin Jonas' life.
2. The man young Noah kills at the start of season 2 is an old Bartosz.
Another theory that directly contradicts the first one is that the unnamed man at the start of season 2 is actually an old Bartosz.
When he starts questioning the Sic Mundus cause, young Noah tells him he's lost his faith, and proceeds to kill him. This is possible as Bartosz travels back in time with Magnus and Franziska.
3. The alternate Martha we see at the end of season 2 is the child of Ulrich and Hannah in a world without Jonas.
In a scene where Jonas was with his father, Claudia appears saying that she saw the world without Jonas. So one could assume that she is talking about the other dimension that Martha came from.
Also, alternate Martha has dark hair, and so does alternate Magnus (according to promo pics), which could mean that in the alternate dimension, Ulrich ended up with Martha instead of Katharina, and Jonas wasn't even born.
4. Adam is actually the father of every single character on the show.
During one scene, older Noah asks younger Noah, "Why do you think he named you Noah?", the 'he' indicating Adam. While this could simply mean that Adam assigned names to all his people, it could also imply that Adam is Noah's father.
If we build on that theory, it suggests that Adam is actually the progenitor of every single main character - Noah fathered Charlotte Doppler with Elisabeth, who would go on to give birth to her own mother.
Agnes' direct descendants are Martha and Magnus Nielsen; her great-grandson Mikkel fathered Jonas Kahnwald.
It's also implied that Tronte was the illegitimate father of Regina Tiedemann, who gave birth to Bartosz. So if Noah and Agnes are Adams' children, then pretty much every single character is descended from Adam, making Jonas his own great-great-grandfather.
5. Alternate Martha is Eve in her dimension, just like Jonas is Adam in this one.
If there's an Adam, it's only logical to assume that there must also be an Eve, especially if we build on the earlier theory that everyone is descended from Jonas' Adam. Considering original Martha got shot and killed however, we have to assume that Martha transformed into Eve at some point, travelling between world, through different timelines, and having a bunch of kids with Jonas/Adam. However, it remains to be seen if she too is evil, or if she turns out to be on the side of good.
6. Aleksander Tiedemann is the son of Jonas and Martha.
Aleksander Tiedemann's real name is actually Boris Niewald. He is one of the few characters whose backstories has still not been properly explained.
According to some Redditors, his last name could likely be a combination of 'Nielsen' and 'Kahnwald', possibly making him the son of Jonas and Martha.
7. The world that alternate Martha comes from is the 'world without time' that Adam has been trying to create.
We don't exactly know everything that Adam has been up to during his timeline, only the bits and pieces that we get during other people's interactions with him. Mainly, we know he wants to create a world without time. If Adam succeeds in a part of his timeline we haven’t seen yet, then this other world would already exist, because it exists outside of time. This might be where alternate Martha comes from.
8. Alternate Martha sent Detective Clausen to Winden to inadvertantly trigger the apocalypse.
The handwriting on the letter from Martha that young Noah gives to Adult Jonas almost perfectly matches the handwriting on the letter that Detective Clausen showed to Aleksander during his interrogation. Clausen also mentions that he received the letter from an anonymous source, and that it informed him that the mystery around his brother's disappearance could be solved at Winden.
Going by the handwriting, this could suggest that Martha sent it to Clausen to trigger the apocalypse for some reason.
9. The town of Winden isn't actually supposed to exist and will be erased.
Redditor arnav1311 theorised about how the only way to untangle the mess that is the city of Winden is to get rid of it entirely. He said,
I think Winden isn't supposed to exist. Winden, the city itself is a paradox. Every citizen cannot exist without time travel and it's all tied up in a loop. Winden is the problem and the show, I believe will end with Winden never having existed.
Well, that's a lot of mind-bending theories, but unfortunately we won't know anything for sure until the third and final season comes along. Until then, all we can do is keep trying to figure out who's who, what's what, and when's when.