Shugo Chara/WMG

The Guardian Charas are related to the Imagin
They're born out of one's desires, can possess people without their permission, and usually tend to bring a change in hairstyle. Sure, the Charas can't time travel, but that's because they are to Imagin as fairies are to humans. Both of them can also take on other hosts if the conditions are right. Eru has transformed with Amu a few times (sort of like her version of Wing form) and Momotaros has taken over Wataru (of Kiva's) body.
 * I declare this theory TV Tropes Made of Win Archive.
 * This troper always thought of them as being more related to Stands, only visible to those who had them as well, capable of gifting amazing powers, that sort of thing.
 * That's what I thought too. Especially with Koichi's Echoes, which was born from an egg and caused a change in his hairstyle and personality.

The Shugo charas of persons, who have more than one, will eventually merge into one, or dissappear until only one stays as the character development progresses
The Shugo Charas always reflect, what the believes and dreams of a person are. If two dreams adjust to each other (for example, let's imagine Amu becoming a CHEARLEADING IDOL SINGER! WOOO!) that must have effects on theShugo chara as well. On the other hand, if that person grows up and realizes, that he or she can't really do it all, all "unneeded" charas will go back into their eggshells and eventually dissappear. (Nagehiko's Temari already went back into hers, because Nagehiko knows, that there's no need to be a Yandere/Yamato-Nadeshiko hybrid, when you're a boy). My question: If Amu likes her 4 charas as much, as I think, how will she get over it if at least two of them (I think, she will lose Suu and Miki in any case) suddenly say "You don't need me, you've got another dream" and go POOF?! Shouldn't finding her true dream make her happy? PARADOX anyone?!
 * True and complete happiness is impossible, that's why. It's like playing a game where there's no way you can have One Hundred Percent Completion, because some events nullify the others.
 * Maybe they become personas. Just a thought.
 * I think Dia actually represents Amu desire to achieve all her dreams, and thus keep all her Chara's. Since this is logically harder than achieving just one dream, Dia was much harder to awaken. The fact that Amulet Diamond recently evoled into Amulet Fortune, whose hairpin features all four Chara's colors, supports this.

The "former King" is Tadase's father
He left the family, when Tadase was still a baby, so he could watch Easter's activities. He will play a vital role in causing their downfall.
 * Jossed. He's actually Tadase's mother's brother, i.e., his uncle. His father was shown in some of the later chapters.

At some point in the future, Nagihiko's family name changes to Saotome.
There's no way he and Alto aren't related.

Yes, but the other Saotome
I mean, he's a crossdresser and one of his Chara Naris essentially turns him into a girl! He HAS to be related to everybody's favorite Gender Bender!
 * I would have guessed Ranma was more a current relative, actually. Especially given the time difference. Nagihiko's family is weird enough to be related by blood to the Saotomes.
 * What was Nodoka's family name before she married Genma? It wasn't revealed was it?
 * He doesn't becomes a girl while transformed in Yamato Maihime, he just becomes the heck of a Wholesome Crossdresser.

The true purpose of the Humpty Lock and Dumpty Key is to cause Instrumentality
The locks lowest level ability is to jumpstart Chara Naris, regardless of how long the Chara and bearer have known each other. This could be seen as dissolving the barrier between Chara and bearer. Its second ability is to allow Chara Naris with other peoples Chara. While not perfect (Dia and Eru are much stronger when used by their original bearers) it effectively means fusing with part of another person's SOUL. Finally, when the lock and key are put together, it lets Tadase and Amu see into Ikuto's memories. Taken to its logical extreme, the lock and key will eventually dissolve all the barriers between people, creating a shared consiousness with all souls combining into one. When that happens, clones of Amu will sweep across the world and turn everyone's bodies into Tang.

The first King, Tsukasa, is Tadase from the future
It has been implied that Amu's chara Dia can facilitate time travel, and, let's face it, Tsukasa looks exactly like an older version of Tadase. So it really doesn't seem like that big a stretch to consider that the helpful but mysterious Tsukasa could be sweet little Tadase all grown up. What purpose he might have for traveling back in time, however, varies from guesser to guesser.
 * This theory is given even more credit as of the last chapter where
 * But under one of the previous WMGs (the one about Tsukasa being Tadase's father), it said that Tsukasa is Tadase's uncle. But if Tsukasa is Tadase from the future, then that means that Tadase is the brother of his own mother. Weird.
 * If Tsukasa really is both Tadase and the first King, the Fridge Logic is even more damning. Tadase has to effectively transplant his entire life some twenty odd years backwards in time almost immediately after graduation in order to still be able to pass for a fifth/sixth-grader and create the legend of the first King, maybe get adopted by his mother's family or something and grow up into Tsukasa. Which is a pretty tall order for a 12-year-old, and also makes him technically Tadase from the past...
 * Or Tadase is the child of his mother and his grandfather (who would also be his father), which would theoretically make Tadase his own uncle. Then, future!Tadase (aka. Tsukasa) went back to the past so he could interact with his former self. See? It makes perfect sense!
 * Either that, or Tadase is a Time Lord.
 * Jossed. It is only a case of Generation Xerox, it is pointed out that they only look similar, but aren't identical either.

All of Shugo Chara! is just a hallucination of Nobuko Saeki, the fortune teller
Nobuko Saeki is the only adult that can see Charas, right? The only other people that normally see charas are children. Nobuko Saeki could be an insane woman who is regularly visited by neighbourhood children (the guardians, Utau and Ikuto). She claims to see little people floating on their shoulders, and the children just humour her by pretending to see them too.

Nagihiko is a MTF transsexual
She is biologically male but thinks of herself as female.
 * Or maybe it's the other way around..
 * Or maybe s/he is bi-gendered, or something else that falls under "gender queer."

Utau once auditioned for Hello! Project
Before the events of the anime (and by extension, the original manga), Utau auditioned for it, hoping it would free her from her commitment to Easter, and she would have been chosen, but Easter found out about it, and ultimately put an end to it, threatening to hurt Ikuto in some way if she tried a stunt like that again. Considering H!P's involvement in the anime, it wouldn't be surprising if that did happen. Oh yeah, she would have still tried to find the Embryo in order to save Ikuto. Above all else, that would still be her first priority.

Yaya is Ahiru reincarnated
Think about it. Overly cheerful, decent yet clumsy ballerina, uses ducks in her attacks... Heck, they even get some Ship Tease with stoic green-haired guys. Okay, they may have some different traits, but reincarnating does that to you.

Tsukasa is actually Laplace no Ma
They are both the kings of the no-answers of their universes, and are able to teleport to different places. For example, the final battle in Shugo Chara Doki: It is stated that Tsukasa went to the amusement park before the Guardians, but did he got inside of there if the gates were locked?