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.
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 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.
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.
Special: Neos United (Upcoming)
YYGDM The Movie: Valkyrie Advent (Upcoming)
YYGDM The Movie: The Wrath of the Defiants (Upcoming)