Absurdly Spacious Sewer: The Catacombs of Paris are sometimes improbably shaped and located (especially when the entrance glyphs are sometimes placed on ROOFS of buildings, yet the tileset for the catacomb in question will still be an underground one).
Artistic License - Geography: The in-game Paris is significantly condensed from the real one, but all the major streets and squares are represented, complete with landmarks and little historical tidbits like their prior (and future) names and historical significance.
Bechdel Test: Passes, although barely. There are three major named female characters, they do regularly converse with one another, but rarely without the presence of male characters, and when they're alone, while they DO talk about marriage, that's not the only thing they discuss.
Lautrec himself. He does surprisingly little... well, doctor-of-natural-history-ing, and on many occasions goes into lengthy rants about why he's superior and different from all those run-of-the-mill 'adventurers'... yet most of the time the only thing he does is adventurer-ing. And unlike Indiana Jones, he doesn't have anything to show for it for the museum's benefit afterward, since the Treasure Animatus he recovers is deadly. It's a miracle he keeps his job.
Gustav is actually a shrewd businessman, it's just that he spends too little time in the office and too much time traipsing about adventuring. Lautrec tricks him into going back to his office at one point to prove it.
Faceless Goons: The titular Knights all wear iron masks and long flowing robes that entirely mask their shape, giving them an inhuman appearance. This goes into ridiculous territory when you learn that there's more than one order of the Knights...
Fleur de Lis: Used in several variations as the insignia for all the orders of the Knights you run into, as well as to denote the entrances to labyrinths and as the sigil on the Treasure Animatus containers, puzzle doors, treasure chests... Sigil Spam at its finest.
Follow the Leader: The core of the game feels very firmly based on the Professor Layton games with the top hat-wearing historian protagonist that goes around claiming "there's no mystery he can't solve", solving puzzles and combating shadowy secret societies. The meat of the game, however, also includes elements from Konami's own Boktai and, as such, it's a lot less of a direct copy.
To make things worse, the first Layton game for the 3DS added very similar action-puzzler block-moving enemy-avoiding elements.
Gameplay and Story Segregation: The game mostly averts the mechanics associated with this trope and its subtropes, but does fall into it a couple of times nonetheless.
Arbitrary Headcount Limit: Justified. You can only carry (and therefore use in battle) up to three Treasure Animatus at once into a labyrinth, but that's practicality, since the items vary in size between hairpins and suits of armour.
Separate, But Identical: Justified. The Knights used to be one order before splitting into factions. They may dress different and act different in cutscenes, but in gameplay they are identical, since they all share their outlook on treasure hunters.
Take Your Time: Even though the plot implies that you move between the plot dungeons of Chapters 4, 5 and 6 with no dawdling in-story, you're free to do as many side-quests before moving to the actual story portion as you please.
Impact Silhouette: Gustav does this at one point, complete with the outline of his hat and all. Lautrec and company use the hole as an emergency exit.
Infinity+1 Sword: There are four, one for each of the "main" spirit types, available in the jewel shop from around the middle of the game. You will only be able to afford to buy ONE of them in a single playthrough and only if you managed to complete ALL of the optional dungeons with perfect or near-perfect results in battles and found all of the treasure chests - there simply is just barely enough gems in the game to afford them. With luck, you'll get them before you do the final, hardest, optional quest. Without luck, you'll get them before the The Very Definitely Final Dungeon. Without any luck whatsoever, you'll only save up enough gems to afford them in the post-ending play (you don't actually need them that badly to defeat the final boss).
Like Reality Unless Noted: All the historical events happened (and keep happening) as they actually did. Treasure Animatus generally don't do anything supernatural other than kill people that touch the cursed objects, and while some of them are rumoured to possess supernatural powers or grant them to their wielders, absolutely none of them come to pass once Lautrec and Sophie obtain them, usually to Sophie's chagrin. The only illogical objects in the game are the guns the villains use... which don't reliably work, just as one would expect from a steam-powered Gatling gun.
Lower Deck Episode: Although you're always playing the game as Lautrec and Sophie, several sidequests focus on (and consequently contain dialogue mostly from) Claude, Milady, various people from Sophie's past...
Nice Job Breaking It, Hero: At one point, Lautrec and his friends catch up to the Big Bad as he's stumped by the fact that the hints that drove the plot thus far have come full circle and point back to where the first one was discovered. Lautrec then proceeds to deduce the error they've made and figures out the next step, announcing the solution out loud... while still standing next to the Big Bad. Who promptly thanks Lautrec for doing his job for him. Sophie's reaction borders on What the Hell, Hero?.
Old Maid: Milady constantly jokes at Sophie's expense that her running around adventuring with Lautrec has already turned her into a Christmas Cake.
Only Smart People May Pass: The entire purpose behind the riddles in the treasure maps and the puzzle locks on Treasure Animatus chambers.
Our Treasure Animatus Is Different Well, they're pieces of treasure cursed and haunted by ghosts who you must fight to tame using other pieces of treasure. To make things more interesting, most of the effective ones are being haunted by ones of their own, so.... likely.
Period Piece: Welcome to the Paris before the Eiffel Tower was built... or rather, as it was WHILE it was being built.
Schizophrenic Difficulty: The difficulty curve rises very gently until you visit the Bastille. Therein, it jumps through the roof on the whole shebang - the puzzles, the stealth levels AND the spirit-taming. Once you clear it, it returns to where it was before, making this a whole-chapter-shaped Wake-Up Call Boss moment, with the Treasure Animatus at the end serving as an actual Wake-Up Call Boss.
Shown Their Work: You have a virtual Paris of the 1880s at your fingertips. You can visit EVERY street, view a panorama of it, and are regularly fed large bits of the city's history through casual dialogue, plot dialogue, sidequests and the journal. About the only thing that breaks the mood is the use of modern-day colour photographs of the city in some of the puzzles and all the landmark journal entries. It should be noted that if particular modern-day buildings weren't there in 1889, they aren't there in the game, and vice versa (complete with an appropriate note in the Journal's info section if the building is/was of importance). Yes, this game teaches you how a city's appearance changes through the years.
Stealth-Based Mission: You've got no weapons, (and killing the police wouldn't look good anyway, since they're looking for a reason to arrest you) and the cops run faster than you while chasing you, which they don't stop until you leave. It's better to just sneak past rather to trying to rush things.
Steam Punk: There are shades of it, particularly in some of the machinery used.
Tactical Rock-Paper-Scissors: The spirit types. Arboreal has no weaknesses and no strengths. Gems are strong against Humanoid but have poor stats that make them near useless against the other types. Aquatic, Terrestrial and Avian form a circular rock-paper-scissors with Humanoid jammed in the middle to spice things up. The game happily reminds you which trumps which whenever you look at a spirit's scorecard.
Wake-Up Call Boss: The spirits guarding the Plot Coupons are tougher than normal spirits in general, serving as bosses of sorts, but the one under the Bastille takes the cake. Clearing him without losing any spirits of your own is going to be a challenge.