As the Good Book Says...: Mephistopheles quotes the appropriate Biblical text from the Book of Revelations whenever he transforms someone into one of the Four Horsemen.
Bodyguard Betrayal: Johann Faust betrayed Elizabeth Balthory of the Chessmon Kingdom, working with Mephistopheles in exchange for Balthory being made his queen. It didn't end well for him...
Headbutting Heroes: Bedivere and Caradoc, with two different views of being a hero. Bedivere and Michael, over conflicting views of leadership.
Horsemen of the Apocalypse: Mephistopheles has been summoning them. War and Conquest have appeared so far as Svarog and Thor, respectively. More recently Mephistopheles seems to have chosen Duo to be Death, but whether he'll succeed or not is unclear.
Invocation: Several characters have digivolution chants as a means of centering their focus.
My God, What Have I Done?: Caradoc recently got one of these, (minus the My God) concerning the destruction of the Chess Kingdom by Conquest/Thor, which he sees as his fault. Had he not tried to be a hero, Mephistopheles wouldn't have had the chance to corrupt Thor into Conquest, breaking a seal and resulting in the deaths of thousands of innocents.
Oh, Crap!: All the damn time, but especially when Mephistopheles starts a chant with the words 'I looked, and there before me was a white/red/black/pale horse!'. Both for the characters and the people reading this. Fortunately, in a warped way, this can only really happen a maximum of two more times... hopefully. Also, any time Kamotz pulls one of his infamous plot twists in a way that benefits Mephistopheles. Which happens a lot.
Tiwaz reveals that the names of his two sons are Campion and Thlayli, both characters from Watership Down. Tiwaz himself is an inadvertant shout out to Bigwig (AKA Thlayli) from Watership Down. Word of God says that as he was reading the book over a course of a year, he realized that Tiwaz and Bigwig were very similar in terms of personality, so he ran with it and had Tiwaz name his children after Bigwig and, another character who Tiwaz would have respected had he been aware of the book, Campion. Tiwaz's secret soft spot for rabbits is also a nod to Watership Down.
When Bedivere is discussing Caradoc's unreliability with Pyra, he makes the following statement 'You say something like 'all present objectives have been cleared', and then a white knight comes charging from nowhere to ruin everything... that's chaos.' This is a reference to Code Geass, specifically a recurring instance of Tempting Fate on Lelouch's part. This is a trend which Storymasterb has admitted he finds particularly head-desk worthy about Lelouch.
The mysterious chant which is somehow connected to Caradoc is actually the battle prayer of the Grey Knights, altered slightly for context.
The Chains of Commanding: Bedivere is reluctant to give up command to Michael, who is more capable of leading the Peacemakers against the threat of demons. Thor feels the weight of kingship as the new ruler of Asgard.
The Reveal: So many it hurts. Many things in Unholy Crusade get revealed as things of significance. Guinier and Kole's evolutions to Megidramon and Apocalymon, Lancelot's murder of Galahad, Sha and Samael's Demon Lord fight, the whole Crusade and many others are revealed as Seal-breaking events, tying into Mephistopheles' plan to break open the Inferno.
Weapon of Choice: It's Digimon, so all different species have weapons that somewhat reflect their character.