Digimon Adventure/WMG

Kari/Hikari is Kira.
Based solely on the fact that Hikari means "Light" and her family name is Yagami. Also, her English name is "Kira" with two letters swapped.
 * This scares me... But Hikari looks to cute to be Kira... Then again, her connection to the Digital World explains Light's hacking skills.
 * For me, this has become canon.
 * Having been nearly drafted by Dagomon to become a wife, she decides later on to have a sex-change and making herself scarce. Then again, we are not told what Taichi's Dad does, but this could mean that Taichi disappeared ... somehow.

Hikari is not an ordinary human
She seems to have some kind of ... powers. She can recall very early childhood memories and seems to feel what other people are thinking (before her Plot-Relevant Age-Up, of course). Her powers left her, when she grew up.
 * Her powers didn't leave, they were redirected. All the crest bearing Digidestined had powers, hers were just the most obvious. However they redirected the power of their crests to protect the Digital World instead of their usual manifestations.

Hikari is Yggdrasil

 * Hikari's light is similar to the light of evolution. Yggdrasil through out the series has used hosts such as Daimon Suguru and Mikihara Norn. Yggdrasil has been shown to power up people.
 * One word "Homeostasis".

In an alternate universe, Kari is Kairi.
Aside from the fact that they look scarily, scarily similar (This troper saw a commerical for Kingdom Hearts: Chain of Memories years ago; Kairi was featured at the very end. I seriously thought she was Kari), as well as their similar (Romanized/English dub) names, Kairi wasn't born on Destiny Islands/whereever it is that Sora and Riku grew up. She also said at the beginning of the first game that she doesn't remember her hometown, leaving her origins up in the air. Also, amongst the Digidestined, Kari is rather special. Aside from abilities mentioned above, her crest, Light, is the only crest that can't be immediately interpreted as a character trait. Kairi is one of the seven Princesses of Heart, and has a pure-hearted personality. So, in an alternate universe where the events of Digimon Adventure and Adventure 02 never happened, Kari was sent to live with her grandma on the islands for... whatever reason. There, she met Sora and Riku, and since they were pretty little then, Sora couldn't pronounce her name right, so he started calling her "Kairi" and the nickname stuck.
 * Except it's been known since the first game she came from Radiant Garden/Hollow Bastion. Remember when her grandmother was telling her the story in the castle library?

Digimon Seasons 1 and 2 are a TV show in the EVA world.
Agumon's upper digivolutions look like EVA, and the light-hearted message of banding together with your friends, some of whom look weird and have self-esteem issues, to fight scary, evil monsters is meant to help the general public accept the existence of the EVAs and NERV (someone's gonna ask where those big robot-things come from, right?) as part of the battle for good. Gendo is a fan of the Digimon Emperor, who he emulates by wearing glove and acting like a BAMF.

DemiDevimon is the reincarnation of the Devimon that Angemon defeated.
After all, it's stated that all Digimon reincarnate (often without their old memories), and Demidevimon seems to have some animosity towards TK and Patamon in particular. Perhaps he has some lingering anger in his subconscious towards the Digimon and Digidestined who killed him.
 * I hate to piss on your idea, but I think it's been Jossed by the sequel series. Ken, as the Kaiser, finds Devimon's lingering spirit in a dark area of the Digital World, and uses it to create Chimeramon. Notice the Devimon arm, with the Kuwagamon and SkullGreymon arms. It's also, at least in the original, I believe (it's been a while since I've seen either version), the reason Chimera went batfuck and rogue.
 * I hate to piss on your pissing, but he can still be right, even with what you said of 02 being true. The way I've always seen it is that the data Ken found in the Dark Ocean to create Chimeramon was the excess which was left behind (memories, power, form) of Devimon after his defeat, and the Digitama he was reborn into was just his basics. He was literally stripped of the added data and "rebooted". So, in a way, the Dark Ocean could be a graveyard for the memories of dark Digimon; a sort of hell if you will. The Digitama hatched, and eventually became DemiDevimon, who still had a lingering hatred for those who had killed him, which caused him to see Takeru and Patamon as greater enemies than the other chosen children.
 * Actually, it doesn't need to be this complicated, since in anode/cathode (a canon wonderswan game), devimon was ressurected. So, the original devimon could have been killed, reborn as demidevimon, eaten by myotismon, resurrected by milenniummon, killed beneath the ocean and then become part of kimeramon. Of course, that explanation only works if the demidevimon in anode/cathode (who is never explicitely said to have resurrected) is a different demidevimon.

The Four Dark Masters are the Four Horsemen of the Apocalypse.
Besides the fact that Devimon (the Devil) started the apocalypse and the 666 imagery/dead rising (zombie behavior, vampirism) type stuff surrounding VenomMyotismon (the Beast of the Apocalypse), AND the fact that Apocalymon immediately follows them--they have specific imagery identifying each of them. MetalSeadramon's episodes make significant use of food and hunger, Puppetmon is accompanied and served by Kiwimon, who strongly resembles a plague doctor/shoots little plague doctors as his attack (Pestilence), Machinedramon leads an army against the Digidestined and utilizes strategy for more efficient plans at their destruction (War), and Piedmon expresses a desire to kill everyone quickly and painfully...preferably alone (Death).
 * I will actually accept that. Now that I think about it, I wonder if they could've been their actual reason?
 * Combine this with the above theory that the Dark Ocean is a graveyard of sorts for evil Digimon. The data of each Dark Master pooled together in the ocean, eventually building up to a DNA Digivolution/Jogress Evolution to Apocalymon (who was otherwise a Giant Space Flea From Nowhere) when the last was destroyed.
 * But Machinedramon lives long enough to DNA Digivolve with Kimeramon to make Milleniumon.

The real Big Bad is a Hagurumon
Digimon were being controlled by dark gears at least for about half of the show. If you look up for Hagurumon's info, you'll notice two attacks in particular: Darkness Gear and Command Input. While Hagurumon's Darkness Gear summons a literal dark gear to attack its opponent, the Command Input attack actually installs viri on the opponent and attempts to gain control of their movements. Now, being a Child Digimon, it would be improbable for his attacks to do anything more than tickles to higher-leveled Digimon. The logical solution is to attempt to force the gears he summons inside other Digimon and run the viri from within, where their data is more vulnerable. The Black Gears, thus, are just what results in combining Hagurumon's Darkness Gear and Command Input attack. The combination of attacks made the gears strong enough to be able to break through some Digimon's cores, even higher-leveled ones. If we can take it to the next level, any and all Digimon that fell victim of the Black Gears, and a few who weren't explicitly under their effects were just being controlled by an ill-maneered Hagurumon. The responsible for all of the plot, then, is a Hagurumon, which would put it at least above Devimon according to the Sorting Algorithm of Evil (which would also mean he was also controlling Devimon to fight off the kids who were "spoiling his fun"). As stated on the complementary material, Hagurumon can't judge right from wrong, so all the Black Gears thing would be just a game for him, and he stopped playing when he got bored.
 * Furthermore, Hagurumon is the traditional Metal Empire Virus-attribute rookie/child, and could eventually become Machinedramon/Mugendramon in the original virtual pets. It's possible that this theoretical Hagurumon is Machinedramon of the Dark Masters, and eventually fused with Devimon in the form of Kimeramon to become Millenniummon. Coincidentally, on the Tamers WMG page, there's a theory that Season 3 was a Xanatos Gambit of Millenniummon's.
 * Which would also make sense. Hagurumon's "playing" with peoples lives remained as he Digivolved and grew, despite becoming able to judge right and wrong, eventually becoming the basis for Machinedramon's cold-blooded sadism.

Piedmon made the other three Dark Masters
Piedmon was the only one created from Apocalymon's chaos on the Digital world, but he is also the only fully organic member of the group. MetalSeadramon is a cyborg, Puppetmon is a wooden puppet with gears and such inside him, and Machinedramon is a robot. Piedmon created the other two to be his allies but was smart enough to make them weaker than himself to keep on top.

The Greymon from the Adventure movie is the same Greymon that fought Tai's partner in episode 16, and was the partner digimon of one of the first Digi-Destined mentioned in episode 53.
An Agumon is shown (in silhouette) standing with the original five Digi-Destined that Gennai tells the kids about before their battle with Apocalymon. At some point during the original group's adventures in the Digital World, that Agumon was killed in a battle, but instead of its egg reformatting in the hands of its partner it instead wound up with young Tai and Kari. After hatching, evolving to Greymon and fighting Parrotmon, it returned to the Digi-World and was eventually enslaved and brainwashed into being one of Etemon's lackeys.
 * This is now my official headcanon. It actually makes sense considering that it's confirmed that Tai had two different Agumon (one as a child, and the one we see in the anime). Also makes for an epic Tear Jerker.

The Black Gears were used before the children arrived on File Island.
Alright, so, I've started watching the series over again, and I recently watched episode 5 again. In this episode, the cast finds themselves in a factory that "builds nothing", as Yamato put it. The Black Gear that infects Andromon is shown to be lodged within the workings of a machine, not flying through the air like the others seen through the course of the first arc. This makes me think that either Devimon had been plaguing the Digital World with the Black Gears before the children arrived (this one simply got stuck in the machine earlier), OR another Digimon had used the same method in the past (this one had been stuck in the machine for some time). We've seen that the factory that Andromon protects is rather large, so it would take him some time to survey the entire building for something as simple as an out of place gear, making the latter far more likely.

Taichi is Spike Spiegel's Dad, or ancestor
They both have the same hair.

Adventure is a sequel to V-Tamer 01.
Taichi, Neo and the other kids had their memories erased at the end of the manga in order for them to live a normal life. Zeromaru hatched early, and at the end was reformatted into a Koromon....that ended up on File Island with some new friends. Unfortunately, the memory thing backfired horribly when Millenniummon unleashed Apocalymon and Tai was dragged into a new adventure with none of his previous memories to aid him.

Myotismon was the fifth dark master
The gate to the human world, and the pedestal needed to activate it, were originally in Gennai's base, before it got taken over by the dark masters. The next time we see these items, Myotismon has his hands on them. Since it is doubtful the dark masters just handed them over, and myotismon doesn't have the power to take on 4 megas, the only conclusion is that he was part of the dark masters. In Venomyotismon form, he would fit in perfectly powerwise.

If Tai had chosen the wrong card to get through the gate, the gang would have ended up in The Pokémon Universe.

 * Not all fans each series were rivals, who hasn't dreamt of an epic crossover series?

Sora is half-vampire

 * From Headscratchers: At some point in the past, Sora's mom had an affair with a Japanese Vampire, resulting in Sora. Her vampiric heritage gifted her with Red Eyes and various stealth-enhancement capabilities, including radar suppression. She instinctively invokes these abilities for herself and her "covenmates" in stressful situations, so as to avoid detection by potential enemies. Unfortunately, instinctive reactions suck at distinguishing between coven-separation (File Island, Tai's Sabbatical) and abduction (the Upside-Down Pyramid), making things difficult for everyone until some point during Tai's Sabbatical, when she learned to consciously control them.
 * Evidence:
 * Sora is the only character with completely inexplicable coloration, the rest having viable, real-world compliant explanations for theirs:
 * Taichi, Hikari, Mimi, Daisuke, Iori: Brunettes, brown-to-black eyes, parents shown to be brunettes. Genotype plausible, phenotype same.
 * Yamato, Takeru: Hair of Gold, Blue Eyes, quarter-French. Genotype plausible, phenotype stretch.
 * Jyou, Miyako, Ken: Stylized black, siblings (if any) shown to have same. Genotype plausible, phenotype same.
 * Koushirou: Dark red hair, black eyes, adopted (do we ever really see his birth-parents in Flash Back?). Genotype plausible, phenotype stretch.
 * Sora: Light red hair, Red Eyes, mother noirette with dark eyes, father graying brunette with dark eyes. Genotype highly improbable, phenotype same.
 * Aforementioned stealth-enhancement.
 * Offscreen stunts of ridiculous physical proficiency:
 * Mount Infinity: Birdramon was too close to the rock to recover from that fall on her own.
 * Mimi's "Queendom": The grounds of the castle were being competently patrolled, and Mimi's room was on the third floor, at lowest.
 * More to be added as I think of them.

The Greymon/Parrotmon fight was indirectly responsible for Matt and T.K.'s parents' divorce.
In a flashback, T.K. keeps telling his mom about the "monsters" and it's bothering her so much (at least according to the English dub). T.K.'s fascination with them gotten to the point where the school was concern about it. The parents paid the teacher and/or principal to discuss it. However, the discussion gotten off-topic as the parents vented out their anger and frustration over each other. And this eventually led them into divorce. Matt overheard all this. While he still deeply cares for his brother, deep down he always resented him for causing their parents to split up.

Joe's parents made a cameo in Episode 38.
In episode 38, we see the Digi Destined at the Convention Center checking on their comatose parents. We see each kid checking on their respective parents and the Kido brothers are checking on a couple's pulses. Cameo starts at 3:16.