Theresa Gray is called Tessa by most everyone, Tessie by her brother, and Tess by Will.
And Will's sister Cecily is called "Cecy" by Will and later Gabriel Lightwood.
The Ageless: Warlocks are this. They do not age after reaching adulthood, but are not significantly more resistant to physical injury than humans. This is also implied to be the case with the Fair Folk. Vampires are a little closer to Immortality, as they possess Healing Factor, although they can still be killed, most obviously by sunlight.
Will constantly says he's always out drinking and gambling, and that there are a dozen girls who've claimed that he'd compromised their virtue. Jem, however, thinks he's lying to make himself look bad.
Will says the reason Gabriel hates him so much is because he compromised the latter's sister's virtue. But then again, it's Will, so we don't know if that's true or not. As of The Clockwork Prince, it's apparently because Will rejected his little sister's advances (in his defense, she was a lovesick twelve-year-old) and broke Gabriel's arm in public.
Gideon Lightwood towards his younger brother, Gabriel.
Bittersweet Ending: Jem lives, but as a Silent Brother who can only see Will and Tessa occasionally over the next few decades. Will and Tessa get married, but Will dies in the epilogue, leaving Tessa alone. Tessa leaves her children, not wanting to watch them die too. Jem is cured and he and Tessa get together, but Tessa will eventually have to watch him die too.
Tessa Gray is a wide reader and quotes poetry quite often. She has the potential to lapse into Badass Bookworm territory.
Charlotte Branwell is very intelligent.
But Not Too Foreign: Both Will and Jem. They're both half English and half Welsh and Chinese respectively. Will's actual name is Gwilym and Jem's actual name is Jian but their real names are only brought up once or twice in passing and for some reason both seem to prefer to be called by their "British" names.
Will Herondale. According to Jessamine, Will thinks he's Galahad. And it's true.
Jem Carstairs. Also, according to Jessamine. Not as much as Will, though.
Clockwork Creature: The automatons - humanoid clockwork creatures that answer to the Magister and that were planned to be infused with demon energies to create a clockwork army. Only very loosely "humanoid" and many times they are remotely humanoid they lack any facial features, up the creepy factor.
Common Crossover: This series and The Mortal Instruments don't have a huge crossover file yet, but it's steadily building. Considering the fact that this series is really just a prequel and many characters are either ancestors of characters in The Mortal Instruments or present in both series (such as Magnus Bane and various vampires), it's not surprising.
Converse with the Unconscious: A version of this happens in The Clockwork Princess. Will and Magnus have a conversation over a dying, unconscious Jem, in which Will mentions his love for Tessa. When Magnus leaves and Will is about to say his final goodbyes, Jem wakes up.
"I am not dead yet, Will. What did Magnus mean by asking you if I knew you were in love with Tessa?"
Distant Finale: The epilogue of Clockwork Princess takes place in modern day, with Tessa recalling her life with Will, his death of old age in her arms as Jem played the violin, and finally meeting with Jem who has been freed from the Silent Brothers and the two of them starting a new life together.
Subverted. Tessa makes the Magister think she killed herself so that he wouldn't get his hands on her power, but in reality she Changed into a woman who'd died by a gunshot wound seconds before the wound would prove fatal.
Played straight with Barbara Lightwood and her brother.
Epigraph: At the beginning of each chapter (usually hinting at what's about to happen)
De Quincy and Magnus Bane both hint at this about Will.
Of course this applies to Magnus Bane as well since De Quincy was interested in him, "as more than friends". Tessa didn't know what Magnus was hinting at, but that was because such things were unheard of in such a time period... (or just not talked about).
Gaslamp Fantasy: The series is set an alternate Victorian London that contains elements of a Masquerade: things such as magic, demons, werewolves, vampires, etc. wander around in the open - but only people with The Sight can see them.
Gabriel Lightwood stops supporting his father after his father is turned into a demon by the demon pox.
Heterosexual Life-Partners: Will and Jem. So much that even though both boys love Tessa, they are willing to let the other one have her and even if Jem died after marrying Tessa, Will would never pursue Tessa as he feels it would be a betrayal to his friend.
The Infiltration: Having been given absolutely, totally false information that de Quincey is the Magister, the Clave devises a plan to have Will and Tessa enter one of de Quincey's lavish parties where he tortures mundanes like Nate by having Tessa transform into Camille Belcourt. At the sign of de Quincey breaking the Law, Will is supposed to signal the Clave so that they can kick some vampire ass.
Interspecies Romance: Will's parents, a Mundane and a Shadowhunter, Tessa with both Will and Jem, Sophie with Gideon, also a Mundane and a Shadowhunter, Benedict Lightwood and an unknown number of Demonesses, Magnus and Camille Belcourt, a Warlock and a Vampire respectively, Camille again, with her former lover, a Werewolf, and Magnus again, with Woolsey Scott, also a Werewolf. Jessamine also develops feelings for Tessa's brother, Nate, though this may just be out of her desire to be a Mundane.
Though Shadowhunters and Mundanes aren't exactly a different species, they are different enough to qualify. To make a Harry Potter comparison, it is the equivalent of a witch or wizard marrying a Muggle.
Will. He very occasionally strays into Jerk with a Heart of Gold territory, but he really isn't. However, he does shift into Jerkass Façade territory after the discovery that he literally kills everyone he loves. Until it turns out that he doesn't. He's still distant, though, but that's just his personality.
It's possible that Gideon Lightwood used to be this, but in The Clockwork Prince, it appears he got better while he was in Spain.
Legacy of Service: Thomas and Cyril Tanner come from a long line of people who've had a touch of the Sight, which is required for servants of the Nephilim. Needless to say, their family's been serving the Institute for a while.
Jessamine, mocking Tessa: Oh, I must choose between Will and Jem! Whatever shall I do?
Mark of the Supernatural: Warlocks have a distinguishing mark that's unique to each one. Magnus Bane has cat eyes and Ragnor Fell has ram horns, green skin and an extra joint in each finger. Tessa, despite being a warlock, does not have a mark because her mother was a Shadowhunter. This is basically her distinguishing mark.
Mixed Ancestry: Technically anyone of note in this series. Shadowhunters are half-angel half-human, Warlocks are half-demon half-human, Faeries are half-angel half-demon, etc etc.
Muggles: "Mundanes." Which, actually makes more sense here when you think about it. "Mundane" means not sacred, ordinary versus divine. But, in Mortal Instruments it takes on a negative meaning, sounding boring and the Shadow Hunters use it with bad connotations — here it's more friendly.
Mundane Solution - Of the Ass Pull variety, when Mrs. Dark in demon form inside a pentagram can't be touched by seraph blades infused with the divine energy of God, but a falling chandelier kills her just fine. Sort of.
Must Not Die a Virgin: In The Clockwork Princess, Will and Tessa have sex when they are trapped together in a prison cell and believe the Magister is in all likelihood going to kill or enslave them the next day.
Will and Jem. Will is a rude asshole and Jem is a kindhearted nice guy. They even look absolutely different: Jem is all white and silver and Will is all dark colors.
Will and Magnus, considering that Will doesn't really do friends and that, up until that point, Magnus hated Shadowhunters.
In The Clockwork Princess, Magnus and Henry seem to get along swimmingly. Magnus is the only person other than Charlotte to ever consider Henry brilliant and Henry introduced Magnus to glitter, his semi-infamous accessory from The Mortal Instruments series.
Only Child Syndrome: The only characters who aren't only children are Tessa, whose search for her brother Nate who eventually betrays her, and is actually her cousin kicks off the plot, the Dark Sisters, Gabriel, whose siblings aren't seen until at least the second book, and Will whose younger sister comes to the Institute at the end of The Clockwork Prince. Aunt Harriet, who was Tessa and Nate's mother's sister, is dead. Everyone else's parents are either deceased or simply not there, leaving them only children.
Pair the Spares: Everyone gets a fairytale romance at the age of sixteen. Sophie is paired up with Gideon after deciding she didn't really love Jem anyway, and almost from the moment she is introduced Cecily is paired off with his conveniently single brother. Meanwhile, only single characters are killed off (Jessamine, Thomas).
Everyone else suffers from this. And I mean everyone. Jem even mentions that everyone is an orphan. To be fair, this is what the Institute is for. It's essentially an orphanage for Shadowhunters. If any of them had parents, they would be living with them. Except Will and later Cecily, whose parents don't count since they're not Shadowhunters.
The Reveal: Mortmain is ACTUALLY the Magister also, Tessa's dad was a demon who fooled his mom into thinking he was her husband, and having his half-demon warlock baby! BUT this is Mortal Instruments so expect some of this stuff to change as the series progresses.
Ridiculously Human Robots: The automatons - despite walking with a graceless gait, they can pass for normal humans well enough.
Running Gag: "There's no such thing as demon pox, Will!". As it turns out, we find out in Clockwork Prince that Demon Pox IS a real disease, and Benedict Lightwood has had it for years and gave it to his wife, driving her to kill herself in shame. Will is so pleased about being right all along that he sings a song about it.
Sibling Triangle: Played with. Though the main character, Tessa's, love interests are not biological brothers, they are parabati, which for Shadowhunters is quite close to being brothers. There isn't a 'Mundane' equivalent for it.
Spin-Off: The series is an interesting example; both this and The Mortal Instruments share a couple characters, (namely, Magnus and Camille), but they're not central to either series, and all the other characters are new. Plus, this series takes place 200 years before "The Mortal Instruments".
Stock Foreign Name: James and William. Could be justified, considering how common those names were when the story is set.