Season 1: The Wrath of Pharaohmon - The first entry, created in 2003. The Tamers, Legendary Wariors, Duelists, (most of the) Sailor Senshi and the Spirit Detectives are living in Tokyo when an evil digimon named Pharaohmon escapes into the human world and possesses a young boy named Lance, then begins plans of world domination, which the heroes must band together to stop. Starts out a bit rough, but It Gets Better about halfway through, when Pharaohmon creates a simultaneous Cell-style battle tournament and Duel Monsters tournament.
Season 2: The Invasion of the Rajita - The Rajita, alien enemies of the Sailor Senshi arrive and use the power of the Orichalcos to steal the souls of the people of Earth. The Tamers awaken the spirits of the Four Saint Beasts (Suzaku, Seiryuu, Genbu, and Byakko) and receive new powers (and training from the Sailor Senshi) with which to fight. Meanwhile, Kaiba tries to fuse the Digital World with the world of the Duel Monsters, but due to a slight miscalculation, it works a little too well and the Rajita use it to capture the Digimon Sovereigns, leading the DigiDestined to arrive and help the heroes out.
Takes place seven and a half months after The Wrath of Pharaohmon, between Dawn of the Duel and the Ceremonial Battle for Yu-Gi-Oh!, and between the Dark Tournament and Chapter Black sagas for Yu Yu Hakusho.
YuYuGiDigiMoon: Gaiden - A collection of short stories that take place at different points on the timeline. Not really required reading for the rest of the season, but still worth a look.
Side Story: Search for the Kuiper Belt Senshi - Sailor Sedna (the Tenth Senshi introduced in Season 2, is sent on a mission to find the members of her own team, Sailor Eris, Sailor Ixion, Sailor Quaoar, Sailor Orcus, and Sailor Varuna, before the Neo Animamates (The Animamates from the Sailor Moon manga and musicals that weren't featured in the anime) do.
Takes place nearly 3 years after The Invasion of the Rajita, incidentally beginning on the day the IAU revoked Pluto's planet-status.
Takes place two months after Search for the Kuiper Belt Senshi, and is officially post-series for all included continuities, but includes a brief cameo at the end by Jaden Yuki depicting his first meeting with Yugi, placing this story before the start of Yu-Gi-Oh! GX.
Across Dimensions - Crossover with Digimon Fusion Kai and Digimon: Accel Stream (by Chaosblazer). When danger runs amok across time and space, heroes in different worlds respond. The dimension traveling menace Paradixalmon establishes an army with Beyond and the Digital Warlord. Their mission is to find and eradicate every Ascendant, super digital warriors akin to Super Saiyans, to prevent an imbalance in other worlds, but the evil trio also intend to use their powers to destroy heroes.
Takes place 4 months before Summer Diaries. The main cast from Digimon Xros Wars make their official YYGDM/Kai/Accel debut in Chapter 7. Though not a part of the YYGDM, Kai, or Accel worlds, they are now directly involved and tied to these three mythos and each world's heroes. The events take place about three months after the Death Generals and Seven Kingdoms Saga.
Takes place a year after the finale of Taiyoukai Awakening, and about 8 months before Dawn of Chaos.
Summer Diaries Special Edition - The original Summer Diaries chapters posted in chronological order with "DVD Commentary", plus several Gaiden chapters unrelated to the Arcadian Cross plot.
Season 3: Dawn of Chaos - Many many years ago, the Dark God Valmarmon was defeated by the Light God Granasmon and split into seven pieces, which were spread across the Digital World(s). Now, evil digimon led by Madoudramon are on a hunt for the missing pieces in order to bring Valmarmon back to life, and the DigiDestined, Tamers, Legendary Wariors, and DATS must unite to stop them. Meanwhile, the Neo-Rajita, alien survivors who fled to the Digital World, resurface and attack the Sailor Senshi, while the Demon Priests from the Meikai attempt to retrieve the Demon Stones from the Spirit Detectives in order to revive their Dark God, the taiyoukai Arago. To top it off, a group calling itself the Paradais Knights is using technology from the future to hack into Kaiba Corp's satellite to remove the Duel Disks' holographic safeties and force the Duelists, (including those from Duel Academy) into duels where the damage is real. Things look bleak until the Neo Senshi (led by Chibi-Usa) and the Signers arrive from the future to help out.
Set two and a half years after the main events of The Taiyoukai Awakening, and is between Year 2 and Year 3 of Yu-Gi-Oh! GX. For the characters of Yu-Gi-Oh! 5Ds (which in this universe is set contemporaneously with Crystal Tokyo) this story is set after the defeat of the Dark Signers, but before the arrival of the Infinity Trio.
The Siege of GranDracmon - The official sequel to Across Dimensions and second collab project with Chaosblazer. The cast of Digimon Fusion Kai, YuYuGiDigiMoon, and Accel Stream unite to fight the root of the evil: GranDracmon. The Ascendants, the Spirit Detectives, the Sailors, and company must stop him and his evil forces to save their worlds.
Set roughly five months after the events of Dawn of Chaos
Anachronic Order: The chapters of the OVA will be posted chrono-illogically (as they put it). The first chapter is actually the epilogue. Word Of God says that the actual chronological order will be revealed after the last chapter has been posted.
Jaarin Wong, older sister of Henry and Suzie. Being a minor Digimon Tamers character, only got three scenes at most and very few lines. In this series, her status has been greatly upgraded once she became the Legendary Warrior of Water. She's even gained her own A-Hybrid (Kappamon), is a close friend to Izumi Orimoto, and the girlfriend of Sam Joseph, Legendary Warrior of Earth.
Yasmin/Gravekeeper's Assailant: Remember that minor girl who Jaden met in Yu-Gi-Oh! GX Season 1? The one who gave him half of that pendant, which the other half belonged to Atticus? She only had two episode appearances and was never mentioned again? Yeah, her status was upgraded in Season 3 as she played in big part in guiding the Senshi to the Orb of Minos and was Sleipnir's chosen guardian to allow the Senshi to unlock his seal, freeing him and granting the Senshi their Dai-Valkyrie forms.
In Chapter 5 of Summer Diaries Special Edition, Miho Nosaka of Yu-Gi-Oh becomes Sailor Makemake, a Kuiper Senshi. She's been reawakened by Sailor Pluto to find her partner, Sailor Haumea, and fight an army of dream demons called Weepers. In Chapter 16, Vivian Wong of Yu-Gi-Oh reawakens as Sailor Haumea, becoming Makemake's Sailor partner.
Badass Normal: Megumi-shishou. She once took down a horde of 20 attempted rapists with nothing but a broomstick, and as the Okinawan Kobudo instructor to three of the Kuiper Senshi, can easily best them (in their non-powered, civilian forms) in one-on-one combat. It took all three of them working together to defeat her, and even then, it was more of a draw. She also took down several Arcadian drones during the O-Ban festival.
Kuzuhamon (a virus version of Sakuyamon) sort of tries to do this to Inumon by joining the Amazon Digimon, challenging Inumon, then intentionally losing so Inumon will be forced to marry her. Of course, if she wins the fight, she uses another Amazonian law to claim a bested male as a mate. So basically, Inumon's screwed either way. The only way he gets out of it is by Sakuyamon challenging Kuzuhumon for the rights to marry him.
The Four Gods: Several instances. There's the Digimon Sovereigns: Zhuqiaomon, Azulongmon, Ebonwumon, and Baihumon; the Saint Beasts given to the Beast Tamers: Suzaku, Seiryuu, Genbu, and Byakko; and four of the Generals of Valmarmon: HiSuzakumon, MizuSeiryuumon, ChiGenbumon, and KazeByakkomon.
Freaky Friday Flip: Between Usagi and Rei, in the last chapters of Summer Diaries: Special Edition
Manipulative Bastard: Sharon Rivers aka Sailor Charon, Sailor Pluto's Evil Twin sister aka the Manipulative Bitch. Posing as an amnesic Pluto and plotting a gambit against the Senshi and the other heroes. She's definitely a prime candidate.
The mysterious Prophet also takes the cake.
Pharaohmon, Kaiser Ghidorah, and Gamera also fit the bill.
Secondary villains: Rajita General Kuiiza, who implanted false, hateful images of Joey's own friends into his mind to corrupt and turn him into a dark warrior and for using his own subordinates as test subjects for his sick experiments. He even sent Nemesis, Yui Tsubasa's dark alter-ego, to her death in a duel with Yui. What else has he done? Tried to conspire fellow general, Nagah, and convince Kaiser Ghidorah to order for her execution for failing to conquer the Amazon Kingdom. With these accomplishments, this guy proved to be even more of a bastard than Season 2's Big Bad. And that's giving him way too much credit than he deserves.
Confusion is generally avoided by not having the two in the same scene. You can generally tell them apart by who they're talking to. Sam Joseph (Legendary Warrior of Earth) will usually be talking to other Legendary Warriors. Sam Stromberg is always with his twin brother Max, and the two will generally speak one right after the other. (Yeah, yeah, Sam & Max. Word Of God says that was completely unintentional. Besides, since Max is the elder twin, he's always mentioned first e.g. Max and Sam.)
Also, in the latest season (Dawn of Chaos), there are several duplicate digimon. You can tell them apart because each has their partner's initial in a parenthetical after their name. There's Agumon (T)ai and Agumon (M)asaru, Biyomon (S)ora and Biyomon (C)hika, Terriermon (W)illis and Terriermon (H)enry, and Lopmon (W)illis and Lopmon (S)uzie.
Timey Wimey Ball: How time travel works differs depending on who's using it. Chibi-Usa's time travel is generally paradox-free, as history is written as if she had always gone back in time. This allows her to visit the past frequently (as well as bring characters from the present into the future) without worrying about the future changing. That's not to say that the future can't be re-written. In Season 2, Kaiser Ghidorah was able to successfully kill Sailor Moon. (Supposedly, Sailor Sedna originally arrived in time to prevent this, but due to the intervention of The Prophet, Ghidorah was able to delay her enough for his plan to succeed.) When this happened, Neo-Queen Serenity and Chibi-Usa disappear a la Back to the Future. In Season 3, after Professor Frank travels to the past, the timeline is disrupted so much that it causes a temporal wave, which the Neo-Senshi and the Signers escape by entering the time stream before it hits them.
Meanwhile, in the Future: The scenes in Crystal Tokyo/Neo Domino City are set 1000 years, to the day, after the scenes in the present. Also, Chibi-Usa seems to age the same amount between stories that the characters in the present do, suggesting that she always travels exactly 1000 years into the past.