Blood from the Mouth: Happens to Bosch when he is defeated by Ryu for the last time (with both sides fighting as Half Human Hybrids); Bosch asks Ryu to perform a Mercy Kill on him, and spews blood when Ryu runs him through with his own claw.
Also happens to Ryu when Bosch stabs him in the throat with his rapier, full with blanked eyes.
Body Horror: In Dragon Quarter, Nina is not a princess, but some poor girl genetically engineered into an air purification device. It works by shunting all of the pollution to the girl, thus driving the initial goal of the characters to get her to the (supposedly) clean surface. Oh and she had her tongue cut out because machines don't need to talk.
There is also a room full of the failed results of previous attempts (in various stages of development), kept preserved in formaldehyde-filled tubes. This is no doubt intended to make them easier to study by the scientists who are working on this project, and not at all to freak out anyone passing through.
In the Non Standard Gameover, which you get from pushing the D-Counter to 100%, we see a silhouette of Ryu twitching violently, before a dragon erupts from his body, rending it to shreds. You don't see much, but it's still scary as hell.
Bonus Dungeon: Kokon Horay. In order to reach it, the fairy colony must be at maximum level.
Crapsack World: Dragon Quarter's setting was all below ground, where humanity (and everyone else) was driven when a massive war ripped apart the surface. This leads to a series of abandoned tunnels and cramping issues which make Tokyo Underground look spacious, as well as severe pollution issues.
Earn Your Happy Ending: Ryu manages to deliver Lin and Nina to the gate of the sky, however he has a 200% dragon ratio. As the party separates, Odjn releases Ryu from his bond, preventing him from being consumed, and he rejoins the party in the surface with a clear blue sky.
Gameplay and Story Segregation: In successive playthroughs of the game, it's possible to raise Ryu's D-ratio to 1/4, but in-story he's still treated as a low-D grunt.
Money for Nothing: Once you have access to the money exchange room in the fairy side-game, you can make a killing off the currency that fluctuates more because it actually has a fairly predictable pattern.
Elyon: Refusing to open the door to the sky when he was a Chosen of Odjn. He feared that it wasn't his own decision, and this resulted in Odjn breaking his link with Elyon.
Bosch: Being defeated by Ryu. Much of this is because Bosch is a "Well Done, Son" Guy who was pressured to excel and he just can't handle being defeated by a low-D; this leads to a descent from being The Rival to a full-blown Villainous Breakdown.
New Game+: One of the few (if only) games that makes this an active part of the game mechanics. You're encouraged, or even forced, to constantly restart the game. The only things that are kept over though is currently equipped items, skills, anything in storage, and unused party experience points.
Power Levels: D-Ratios in Dragon Quarter determine a person's potential in life and are therefore used as criteria for determining social status and prospects. 1/8192 means you're stuck as a grunt for life, 1/64 makes you a super-elite, while 1/4 more or less marks you as a Physical God. The more accurate description of the D-Ratios is the likelihood of a successful linkup with a D-Construct, but exactly what they base this on is never elaborated on, and while you can raise your Ratio up to 1/4 in a New Game+ by playing through the game quickly, opening as many treasure chests as possible, killing a lot of enemies and getting first strikes on the majority of them, finishing the Bonus Dungeon, saving as little as possible and having your characters leveled up as high as possible, it doesn't effect the storyline and only allows you to explore a few bonus areas and allows you to get a better version of the game's Infinity+1 Sword.
Note that Ryu being rated as 1/8192 means that he has a 0.0001% chance of successfully linking with a D-Construct. The fact that he does, and with the most powerful one to boot, shows that the D-Ratio system is actually not terribly effective at determining someone's overall ability. Ryu is a grunt that has the ability to become essentially a god (and that kills a bunch of other gods in his quest). At least part of the reason he's opposed by the ruling council is because they simply refuse to believe that someone so pathetic could do what he did.
Somewhat averted. D-ratio is a measure of probability. It's still technically possible for a low-D to merge with a D-Construct, just much less likely than a high-D. Conversely, someone could theoretically be a 1/4 and still fail to merge. The game simply doesn't address this issue because there is no need; like most good stories, matters of probability tend to work in favor of dramatic necessity.
Save Token: That were extremely rare, to boot, although there was fortunately Suspend Saves available if you really needed to quit.
Shielded Core Boss: The final bosses and some end-game enemies have what is known as "Absolute Defense", where you have to deal a minimum amount of damage (in the form of a negative damage number) before you actually hurt them.
Suspend Save: Except in the PAL version, for some reason. To compensate, you start the game with 9 Save Tokens, although whether that's a fair tradeoff is up for debate, especially considering the 50-floor Bonus Dungeon with no savepoints whatsoever.
Theme Naming: Mostly ties into You Are Number Six, but there are some additional examples; the Regents mostly have names that are theological references:
Elyon is traditionally a Hebrew epithet for God.note and a bit of a shout-out to Fou-lu, whom Elyon is an explicit Expy of.
Jezuit is a reference to the Jesuit religious order
Tantra is a reference to a specific estatic Buddhist religious school, and Cupid is the Greek god of love.
The Regents and major characters not named after theological references, Russian numbers, or direct shout-outs to the earlier games in the series are named after Greco-Roman philosophers and orators. Zeno shares a name with a famous Greek philosopher who (per the Other Wiki) wrote extensively about paradoxes and the nature of reality, and Hortensia shares a name with an orator who (again, per the OtherWiki) led the Roman Senate to partially repeal taxes on female nobles.
Took a Shortcut: Jaju, Arma and Leo, better known as the storage, armory and item shop kids, do this shamelessly and have no trouble reminding you of the fact that there is no conceivable reason for why they could possibly show up where they do.
Trailers Always Lie: One CM for the game, which uses a lot of beta footage, centers around climactic-looking footage of Ryu facing off with Dva in a large, well-lit room that looks something like the area Odjn is in. Needless to say, this is pretty inaccurate in various ways.
There's also the intro movie to the game with lenghty segment where Ryu slowly walks forward in heavy rainfall while dragging his sword along the ground: while the last part does offer an explanation where the hell the rain is coming from, it doesn't really match up to his surroundings in the earlier parts.
Also, Ryu. He lets absolutely nothing stand in his way. Not his manipulative friends, not his respected superiors, not the long-established order of the world, and certainly not something as meaningless as tradition.
You Are Number Six: Everyone, save for people who are fugitives from justice (Lin and the rest of Trinity), the Regents, or those unfortunates so low on the totem pole as to be legally considered experimental animals (hello, Nina) have a D-ratio officially as part of their name.
Elyon has a number-nickname of Origin, a mathematical term for 1.
Every single dragon in the game has literal numbers (in Russian) as names, based on powers of two. Yes, even Odjn; technically 2 to the zeroth power is 1.