Dresden Codak/WMG

The Telepathic People of Tomorrow in the very first comic are the descendents of the future humans from the Hob storyline
After removing artificial intelligences, and consequently most computers, from their lives, and regaining their sight, these future entities develop new means of improving their lives. So, rather than increasing the complexity of their lives with different types of computer, the rely on boosting their brain power. Didya notice how the background of the far future have no complex buildings in the background, and resort to cannibalism? They obviously have to compensate for their lack of technology with what their massive brainpower gives them.
 * That's not the very first strip. Although the very first strip does also have an exploding head.

Niels Bohr is really dead
The Hobs just have found a way of recreating him in cat form. Alternatively...

The Tokamak siblings are the reincarnations of Bohr
They're "Nuclear Powered", and harness the power of physics. Niels Bohr was vital in understanding the structure of the atom and quantum mechanics. See a resemblance? I do. And that's all that matters here.

Tiny Carl Jung is actually telepathic
Fed up with seeing Kimiko skulk in utter solitude, he harnessed his power to create Kimiko Red, Kimiko's polar opposite in the Myers-Briggs system, to go talk to Kimiko's crush. Unfortunately, this removed most of Kimiko's social skills and morals, rendering her a pseudo-sociopath in the Hob storyline. In addition, when Kimiko cries in the Hob storyline, she's not mourning the fact that she's alone. At least, not in the conventional sense. She's mourning her lost humanity, which either "Died" or "Left".
 * This is brilliant. You should tell Aaron this.

Old Man-Man will beat the time colonists
Old Man-Man (hereafter refered to as O M-M) is the standard superhero, and thusly will save the day. In addition he's a secular humanist, so obviously (note sarcasm) he has a problem with authority, and thusly will have a problem with the time colonists.

O M-M is the father of the Tokamak siblings
Both O M-M and the Tokamak siblings strongly believe in science, and all three believe in one type of secularism or another. Also, all of them are something like superheroes. Coincidence? I think not!

Kimiko was WRONG!
Kim's hypothesis about the Casimir effect and the theory of branching universes doesn't hold up for at least two reasons: chaos theory dictates that the mere presence of the wormhole probe is likely to alter the growth of Earth in a way that would not lead to human development, if history was in fact mutable; also, the time travelers never bother to confirm her theory and, in fact, continue to act as if they were trying (and failing) to avert a Stable Time Loop, which would presumably imply predestination.
 * The changes from the Hob travelling through the wormhole would be incredibly small, given the distance likely, so it is unlikely that it would significantly affect human development.
 * Doesn't matter the size of the changes, butterfly effect = small changes snowball. That's the whole point of Chaos Theory
 * Chaos theory is a mathematical theory about the behavior of chaos. The butterfly effect is a trope, not a law of nature. There is no physical reason why a dormant molecular computer landing in America without causing any damage would affect the development of any organism millions of years and thousands of kilometers away. Perhaps the insect species which had some of their organisms crushed would have had different descendents, but the course of their evolution would have been identical (otherwise it would be impossible for evolution to work, since it can only work on constant effects for generations). The time travelers act as if to prevent a stable time loop, because every element that caused them to get in their situation is present in Kimiko's universe. Apart from the time travelers and Hob themselves, there is nothing that sets the two universes apart.

Kimiko is Sarah Conner
And Hob and the Time Travelers are Terminators.

Tiny Carl Jung is a robot toy or was otherwise created through technology.
It would explain why a bunch of people who seem to pride themselves on their sense of rationalism find nothing wrong with a miniturized version of a long dead quack hanging artound with them.

The Dungeons & Discourse comics are real, the rest are fantasies used to power potent spells.
Except the Hob arc, which fizzled against something's self-indulgence resistance.

Dungeons and Discourse was devised by Tiny Carl Jung in hopes of winning money off the others with his advanced philosophical powers.
Unfortunately, he's not very good at it, and keeps forgetting his own rules.

Hob is a truly evil being from another universe that is made to be an exact copy of the real Hob.
Stable Time Loops aren't the default, and nor is the chaos theory explanation Kimiko puts forth. The Clock Roaches supplanted Hob in favor of a creature that would eventually bring about the given future instead of avert it. The "real" Hob sent from the future is trapped in the other dimension, completely dormant, and the entire thing was dropped in place of Kimiko saving the day from (or in, YMMV) a bad Terminator homage with her mad future-saving full-screen panel skills, and then going back to a perfectly normal life, albeit with slightly more self-esteem and three robot limbs.

Dmitri's Dungeons & Discourse character is a clue as to his true alignment.
And possibly but not necessarily Alina. He's really Neutral Evil, able to resist doing evil for evil's sake until he can get the metaphorical Occam's Razor of the Dread Solipsist, the simplest solution being to defeat everyone in one fell swoop while their back is turned instead of having to fight them.

Everyone except the Kimikos and Old Man-Man are artifacts created by Rupert and Hubert.
They built Tiny Carl Jung and the nuclear-powered Tokamak twins while they were on the moon, and sent them to earth to help Kimiko and the advancement of tiny psychology. Cat Neils Bohr was also made by them (not the original Neils Bohr). Old Man-Man is older then them (because he's older than everyone), and thus not one of their inventions.

Cat Niels Bohr is dead.
His wave function collapsed when the readers observed him, and he can't possibly be alive each time someone reads the archives, because time travel does not work that way.
 * Actually, since Cat Niels Bohr is only one person, his wave function just collapsed into one state (living, observed, mortal) and any future observations will see him in the same state with 100% probability. However, if we were able to quantum mechanically observe the in-comic universe, then the characters could test our existence with a simple physics experiment (draw attention to a not collapsed quantum wave function (in order to get the reader to observe it), and check for collapse). Given Kim would then realize the existence of the outside world, she would have traveled to it. However, since she has not, we can conclude our observation of their universe is not a physical observation. Therefore, Bohr's wavefunction remains unscathed, and he remains unseen. (Further evidence lies in the fact that the comic universe is imaginary, and it is possible to imagine multiple waveforms without them collapsing by your imagination).

Dungeons and Discourse will become a real game.
Please?
 * Seconded. People love Dungeons and Discourse, Love Conquers All, therefore Dungeons and Discourse will eventually exist (Or so this troper hopes with all his heart).
 * The game is now real and can be found here.

Cave Man Science Fiction is actually a play in Kimiko's world.
Preformed by Harvet Ismuth's play group.

Kimiko's father will return
Until Dark Science 10 it was subtle, but the clues have been heavy in this arc that Mr. Ross has died. Either some AI last message or in hiding, he will return. We are talking about Kimiko's father here. He may not be as talented (no way of knowing for sure), but from we have seen of his works due to his money and experience makes it unlikely he didn't have a back up plan. Heck, he might have even faked his death to see how his daughter does in a world where she no longer has her driving force of not being him around.

The Kimiko in Dark Science is not the same Kimiko as we usually follow.
Well, more than simply in the sense of it being some weird Alternate Continuity. Observe: See that guy? Compare him to Dark Science Kimiko's father here. The resemblance seems uncanny (especially comparing the second to last panel of the former and the first panel of the latter), given for the author's currently detailed style. If this comparison has meaning, and we want to avoid weird squickiness, this Kimiko ends up being some sort of bizarre Generation Xerox.

Or it's just a meaningless resemblance (it's not entirely perfect and Dark Science Kimiko's mother is named Serena, not Kimiko). Still...
 * I think Diaz adapts his characters to the needs of the current story, rather than being a slave to exact continuity (for example, Kim's eye color changed from blue to brown, presumably to better contrast with her artificial eye). Also, WordOfGod indicates Hob and Dark Science are part of the same world/timeline.
 * Part of it is just the change in style. Diaz cares enough about continuity that the difference between Kimiko's father in Hob and Dark Science has been rationalized as a cheap disguise. Note the eye color change. Kimiko's eyes always matched her hair highlights. Pre-Dark Science her hair was often black or had a blue tint to it. That tinting/highlighting was also her eye color when her eye coloring was shown. Pre-Hob it was often just pupils. Her hair was likely either never blue, and her hair/eyes were stylistic, or she was into hair coloring and colored contacts.

The strange ceramic creatures that form part of the landscapes are golems
They're silent and generally stationary, they don't seem mechanical, and yet they have such vaguely humanoid shapes. I'd say they're probably made of clay (maybe ceramic). Dovetails in nicely with some of the biblical themes we've seen in Dark Science recently.

Kaito Kusanagi either founded the Office of Opposition before his death, or he faked his death and is now leading it.
Compare this strip to this strip. Both he and Melchior mention a hidden, unsuspected conflict, and both use similar imagery (science and innovation are "crippled" and must occur outside the established system). Plus it would be awesome, plus it would allow exploration of Kim's issues with her father, which are many, varied and deep.

Melchoir can't be entirely correct
There is evidence for his hypothesis at the end of Dark Science, Act 1. Namely that Kimiko is waking up and seeing her father after Hob. This would be the prime time to alter her memories. Still, we seen in events after Hob that some of the fantastic events are still coming occurring, and that the female Tokamak Twin did interact with Ron implying she is real. Add to it that Melchoir, even if he seems more grounded, is from a society that voted to decide Kimiko was a weather balloon rather than to admit a person could actually be appealing. He could just be outright wrong.
 * More to the point: He assumes she's making up the part about being Kusanagi's daughter. That alone suggests that he's not just maybe, but definitely wrong. Probably about everything.