A bit of Fridge Humour hits in the Sequence 1 memory, "High Society". In most stealth missions across the series, including in this game, you get desynchronized if you enter 'conflict' with the tailing target - which means that the Assassin in question never got noticed. However, if you enter conflict while sneaking through the party, Arno just gets kicked out of the gates - which means that Arno canonically got noticed at least once trying to sneak into Elise's coronation ceremony.
Completing Rift missions give you access to Assassin Intel. One of these is a list of potential Sages. One of the entries reads: "David Jones. Nationality: possibly English. Born: Mid-20th century. Status unknown, In the 1970s and 80s a few scattered reports of a man resembling a Sage surfaced. He was said to be "otherworldly", "extraterrestrial", and "possessed by multiple personalities." So far, these reports have proven inconclusive." David Jones happens to be the real name of a certain David Bowie.
Napoleon snarking about Arno's outfit, and how it becomes more and more conspicuous the further the series gets from the Third Crusade:
"The Escape", the last mission of Sequence 9, which is one concentrated Funny Moment. It begins with Elise running in away from Jacobins for reasons she refuses to explain, and escalates very quickly to stealing a prototype hot-air balloon in the middle of a thunderstorm with Arno desperately trying to catch up with her.
Shaun's database snarking is back, now in the form of footnotes. From the entry on Jacques de Molay:
Jacques de Molay was born between 1245 and 1250.* * Now that's a long labour.
The entry on Les Misérables is essentially a rant about how much Shaun hates the musical and the France in Unity is not the France in Les Mis. And anyways, he prefers Cats. Much more believable.
Every paragraph in the story about the Red Ghost of the Tuileries is accompanied by increasingly incredulous notes about the ridiculousness of the story.
I bet you didn't expect to read the phrase "expelled a German butcher" just then. I know I certainly didn't. I think this is the weirdest story ever. An expelled German butcher, with a French name, gets so annoyed he swears revenge. Okay. And then what? Is this a dream? An angry German butcher stayed so annoyed he'd once been expelled from a site that he died and then haunted a palace? What? Marie-Antoinette asked a MAGICIAN to PROTECT HER AGAINST THE GHOST OF AN ANGRY GERMAN BUTCHER? WHAT IS HAPPENING? Am I HIGH?
One of the entries is on the Phrygian Cap, which gives us an interesting look at Shaun's... past achievements.
The Phrygian Cap* was originally a symbol worn by Paris (son of Prima, from Phrygia) that would be taken up in late Roman iconography, well before it became a symbol of the Parisian sans-culottes. * For two years I made someone at school believe the Phrygian Cap was a form of birth control. No real relevance here, I'm just proud.
As you renovate Café Theatre, new rooms are unlocked, each of which holds Assassin records from times older - all of which are amusing.
In the well is the "Progress Report for Initiate Charles Dorian", which makes it abundantly clear who is writing even without the signature.
(The letter is written in a crude hand, as though the scribe were not used to writing)
Here's your goddamned progress report.
Initiate Dorian is showing progress.
We find out that "Devils in the Caribbean" the fake movie they devised at the end of Assassin's Creed IV: Black Flag was released commercially and did pretty badly. Their internal marketing from the Helix Rifts tries to make the best of a bad situation:
Never speak badly of past projects. Spin negatives into positives, E.G. If they say "The film 'Devils of the Caribbean' was a frightful mess of clichés, dime-store moralizing, and pandering stereotypes. Who thought this bucket of bilge water was a good idea?" You say "Certainly we realized very early in production that 'Devils of the Caribbean' would not be the ideal experience for everyone. But for those who want a fun, exciting, and lighthearted look at the Golden Age of Piracy, their ship has come to port."
As horrifyingly Badass as it is when you realize Germain has the Sword of Eden, Arno's reaction is pretty funny; the Sage raises the sword, lightning rips out of the tip of the blade, Arno leaps aside as though he dodges magic every day... and then pauses for a moment, realizing he just dodged lightning. "What the hell was that?" indeed.
Shay's Templar Outfit and Bellec's Assassin Outfit lack Arno's Hidden Blade - purely a graphical effect, but still kind of distracting. If you're using one of these outfits during the last mission and you have the Blood FX turned off, Arno looks like he's Force Choking Germain at the end.