These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Rido. Pure evil, or did he actually use to be a decent guy when you consider that before his madness he'd spent about 3,000 years with Juri and Haruka, while they were a couple? Kind of makes it hard not to sympathize with him when he held out living with his unrequited love for such a ridiculous amount of time, vs both Kaname and Zero who couldn't help but treat each other like mortal enemies from the get-go.
Angst? What Angst?: Yuuki never appears to give a second thought to her real brother who had been murdered by Rido while he was just a baby.
Anti-Climax Boss: Rido. For all that build up, he's rather quickly beaten by Yuuki and Zero with not much apparent effort.
Arc Fatigue: Sara's arc was rather lengthy as well as pretty unnecessary considering how little she achieved in the end.
Ass Pull: Yuuki's blood somehow countering the effects of Sara's blood for no apparent reason, other than to make her "special".
Aido's father's sudden reveal of being alive with no explanation given.
At the end, the solution to coexistence between vampires and humans is to... create a cure that can transform vampires into humans. What?
The author apparently trying to justify Yuuki's Teen Pregnancy at the end by adding the fact that a vampire goes pregnant for 2-3 years, making her older by the time she had the baby.
Badass Decay: Interestingly, Yuuki after she becomes a pureblood vampiredespite the fact that as a human she was completely capable of protecting the school from the Night Class. This trope may go hand-in-hand with the Seasonal Rot mentioned below, since for a good portion of the second story arc, she's obeying her brother/lover Kaname like a good vampire princess and staying neatly in the vampire kitchen. Somewhat justified in that she can't use her anti-vampire weapon any more but unjustified in that she's allegedly one of the strongest vampires in existence - she should be able to figure out some way to fight and protect herself!
Heck, Kaname and Zero suffered from this as well. Kaname starts out as a dark, mysterious and worldly vampire, always knowing everything and seemingly having a plan for everything, fittingly earning him the status as one of the oldest purebloods. Eventually however, all his actions and plans seem to be wishy-washy and poorly planned, sending him into Motive Decay and/or the reasoning that everything is "for Yuuki", which, while romantic to some fans, comes off as weak and pathetic to others who had expected alot more from him. Zero by the end of the second arc may have been an emotional wreck from The Reveal, but he also renewed his pride and refusal to let anyone push him around anymore, making him a badass stoic whom one would have to earn the right to get close to. Towards the end of the story however he's completely willing to be under Yuuki's thumb again, immediately forgives her for having erased his memories and gone back to Kaname following so, and ultimately begs her to say she'll be with him.
Base Breaker: Zero and Kaname, though especially Kaname, who're either the devil incarnate or Jesus 2.0, depending who you ask.
Big Lipped Alligator Moment: Yuuki's out of nowhere giant butterfly wings popping out her back in chapter 68. (Though the butterfly motif does later return to show its symbolic purposes considering her character.)
For the anime; the addition of Zero biting Kaname a second time. Completely unnecessary and irrevelant to the (original) plot (the whole point of Zero biting Kaname the first time was so he would stall his fall to a level E significantly), obviously making it a pure Fanservice addition. And considering the not-quite top notch animation it wasn't even really good for that.
A minor example, but Yagari recently revealing that the level E nurse from Zero's childhood was his fiancee could count. A revelation that came right out of nowhere, and was left as an issue as quickly as it was brought up.
Opinions are torn over whether Zero's speech to Kaname in the penultimate chapter about how the latter should stay alive for Yuuki sake rather than killing himself was a touching example of his Character Development, or a complete destruction of his character, cementing him as an Extreme Doormat.
Zero could be compared to Dante as the white-haired male lead who despise their demonic halves and spend most of their time hunting down monsters, including the ones responsible for the loss of their parents.
Crowning Music of Awesome: While the anime is so-so, the soundtrack have received alot of praise for capturing VK's theme and its characters well. Just listen to Kaname's badass  or Zero's beautiful  theme.
Deader Than Disco: It used to be one of the premier Shojo romance series for quite a while... until Seasonal Rot alienated everybody, including former fans. Now, it's barely remembered at all, except as a warning for future writers regarding the genre.
Designated Hero: Kaname towards the ending, full stop. The man reveals himself to have caused Zero's family massacre, mass murders apparent peaceful purebloods, hides behind another pureblood's body to be injured instead of him, treats hunters like ragdolls, badly wounds Ruka (by a stab that was also meant for Zero) and abandons his servant to the hunters, all the while not showing an ounce of remorse or acknowledgment of doing anything bad. And yet, because he didn't really kill Aido's father, he suddenly gets the treatment of being "innocent" and noble for his intention of becoming the next furnage, while the purebloods he hunted are presented as antagonistic and petty for wanting revenge on him.
Draco in Leather Pants: Kaname. While he has seemingly good intentions in everything he does and genuinly loves Yuuki, he still has a cruel way of treating people, good or bad, by manipulation and even murder with no apparent remorse. Some fans still sees him as a saintly character who're only "misunderstood", or whom has the right to treat people how he likes, it still doesn't give him antagonistic qualities.
In-universe as well, with Yuuki's perception of him.
Dude, Not Funny!: In a short bonus, a random day class student has a crush on Yuuki and plans to give her a love letter. Cue Kaname being mad to the point he rips open a tree with his fingers and threatens to kill him should he dare to, all while in the state of Tranquil Fury. It's supposed to be funny, but the manner in which it's done made him seem like a textbook example of a Crazy Jealous Guy.
Fandom Rivalry: Do not compare Vampire Knight to Twilight. Just don't, unless you want to be attacked by a mob of angry fangirls. There seems to be a strong dislike against Meyer's sparkly vampires within the VK fandom.
Fanon Discontinuity: Fans in general had been growing weary with the Seasonal Rot for quite some time, but the rushed and copped out ending only served to pull the last straw as it was considered badly written by most, butchering all three main characters into sappy, Badass Decay protagonists, repeating the much hated Love Triangle to its last breath and pulling a ridiculously drawn and executed vampires vs. hunters battle hardly anyone could take seriously. While the rushedness of the said ending itself wasn't really Matsuri's fault but the Executive Meddling, it was her inexperience with long-running stories that eventually surfaced to the point she was basically told "The story sucks now, how soon can you end it?" In the end, all this has caused many fans to pretend to, or agree that the second arc should never have happened, and that the story should have ended at volume 9 while the art and storytelling was at its strongest.
Rido x Yuuki (since he calls her Juri, may double as No Yay...)
Zero and Shizuka
Zero and Sara
Does Yuuki and Zero in the second arc count?
Freud Was Right: Although it's obvious, the Kiss of the Vampire serves as a metaphor for sex. Especially with regard to the "secret relationship" between Yuuki and Zero during volumes 3 and beyond. In other words, Zero is "boning" both Yuuki and Kaname. Seen in this light, the final scene with Zero and Ichiru is quite Freudianly symbolic as well.
Not to mention the pretty suggestive faces Yuuki often makes upon being bit by Zero (blushing, closing of eyes, panting...).
Zero is getting into the taste of Yuuki's blood a tad too much here.. 
There's also a one-off Yay scene between Shiki and Ichijou at the latter's birthday party, complete with blood.
Also in a bonus manga in volume 4 Shiki is sleeping on Ichijou's shoulderMatsuri Hino said in a side panel that she should have had him leaning on Rima instead and that "it's difficult to develop love relationships in this manga" (Instead of Ichijo...)
It Was His Sled: Considering how fairly popular the series is, most readers enter it with the knowledge that Yuuki is a vampire.
"My way of loving makes you unhappy, Imma should have given you to Zero."
"Lets have sex, hoe."
Memetic Sex God: Zero and Kaname. All the vampires would probably apply though, which is pretty much a given for a vampire story.
Misaimed Fandom: It's a shoujo targeted towards a young teenage audience, yet its narrative, especially the Love Triangle's, is alot more complicated, dark and subtle than you'd expect a teenage mind would grasp, or simply care about. It's likely due to this that Kaname/Yuuki, while their relationship does have romantic aspects, are first and foremost meant to represent a dark, unhealthy and self-destructive pairing (second arc) where Kaname emphasizes it by pointing out twice towards the ending that he doesn't make her happy, while Zero ultimately is portrayed as the "light" pulling Yuuki out of her and Kaname's "deep, dark forest". Even so there's plenty of their fans who will claim Kaname/Yuuki to be the epitome of true love, and that even though she ended up with Zero, he couldn't have made her as happy as Kaname would have. That or, apparently, happiness isn't important in a relationship.
The "big" battle between hunters and vampires in the final chapters which is hardly drawn out and mostly consists of stick people drawings randomly scattered across panels to apparently present a dramatic and suspenseful fight.Good one.
One True Threesome: The fandom is mostly divided between Kaname fans, who ship Kaname and Yuuki, and Zero fans, who ship Zero and Yuuki. Then there are the ones who say this whole problem could be conceivably solved with a large enough bed...
The final chapter presents this as a canon example, because while it cements Yuuki and Zero as the Official Couple, it equally demonstrates Yuuki and Kaname's devotion for each other.
Namely, Kaname encourages Yuuki and Zero to be together, telling them they "have been shining so radiantly that I've been squinting my eyes at the brightness", however, only a few pages are dedicated to their happy ending. In contrast, Kaname sacrifices himself for Yuuki's happiness and tells her that he wasn't unhappy with her, and also that nothing of what he did was her fault, amidst Yuuki's tears over not being able to help him and begging him not to leave. Therefore, while Zero and Yuuki marry and spend many happy years together, Yuuki also loves Kaname enough to the extent that she gives up her life so that he can live happily as a human, which again can be seen as her way of repaying him the happiness he allowed her in being with Zero.
Ron the Death Eater: Both Zero and Kaname can be subject to this. Kaname, while he certainly has highly questionable morals and falls more or less into Anti-Villain category, has a few redeeming qualities and can be genuinly kind when he wants to, yet are still regarded by some fans to be devil himself. Zero is a through and through Jerk with a Heart of GoldAnti-Hero who is stated to be the story's most kindhearted character, frequently shown by his selflessness and self-sacrificing personality, yet to some fans is nothing but a "hateful racist who abuses his powers, beats Yuuki and whines about being a vampire", and who also thinks he should be, or will become a villain.
Yuuki is also treated as such, often accused of being a slutty and self-absorbed whore who toys with the "totally innocent" guys. Neither of the dudes are especially "innocent" and "flawless", and neither is Yuuki herself - but apparently having cocks and good looks means that all the blame shall be shifted to the "evil girl"...
Seasonal Rot: The second arc suffered from a regression in quality and storytelling, causing the story's popularity to drop to the point Hino Matsuri were forced to shorten it by the magazine it was published in. To put it in an example; the very last volume sold less than half than what the 9th volume (halfway through the story) had done within the same time frame!
Squick: Inevitable for at least some readers given Pureblood romantic preferences. Leads to disbelieving reactions of how Yuuki is perfectly okay with continuing a romantic relationship with Kaname after learning he's her brother.
And it doesn't exactly get any better when it turns out he's not her brother, but her great, great-something grandfather. Yeah...
While it's common to have a thing for incestuous pairings in fiction, some fans take their preference to an extreme by wanting nearly every character to be in an incestuous relationship, that is the ones who ship Kaname with his daughter, said girl with her brother (the foster/children of Zero and Yuuki) or even better; wishing a third Love Triangle will erupt of both Kaname and Zero's son falling in love with the daughter. That's right, some fans like the thought of Kaname falling for his own daughter and competing over her with her half-brother. That or, one comment would point out the observation that if Yuuki had had a son looking like Kaname, she'd end up falling for him. One might certainly hope the makers of these statements don't apply their fetishes to real life...
The Scrappy: Yuuki's inability to choose between the two guys, leading to her two-timing Kaname and screwing over Zero's feelings time and again throughout the story has gained her alot of hate from both sides, and while the guys are far from flawless themselves, it's the fact that Yuuki's stated to be a "just" heroine that ends in too much of a Moral Dissonance.
They Changed It, Now It Sucks: A lot of people are unhappy with how the anime differentiates from the manga, with mediocre art, random order of events, and the characters' personalities being somewhat messed up. Apparently the author herself wasn't pleased with the ending result. Though it doesn't come as a surprise to anyone familiar enough with StudioDeen...
They Wasted a Perfectly Good Plot: You have a story of vampires vs. vampire hunters, leading to a lot of possibilities of focusing on the battles, politics and development between the two sides, which is pretty much put under a bus most of the time to focus on a whiny heroine and what choice she'll make between two hotties, which would have qualified for a Romantic Plot Tumor if not for the fact that it's a shoujo, where the romance is supposed to be the main focus. Still, some more balance could have been put into it.
The Untwist: Kaname is killing purebloods to make a safe world for Yuuki and humans... something most fans had guessed since he first set out on his mission, regardless what side of the fandom they belonged to.
Considering the increasingly horrible things Zero gets subjected to, yet somehow doesn't go comatose from a despair overdose, he fits pretty well into this trope. Could also fit into Woobie, Destroyer of Worlds, at least where vampires are concerned.
As of the second arc, he could fit into the Iron Woobie section as well. For witnessing his parents being killed, his twin brother betraying him and later having to kill that brother, watching the girl he's in love with be in love with someone else, being turned into what he hates the most, discovering said girl he loves is what he hates the most, and then letting that girl go to the guy he hates, he has not shed a single tear or complained about how pitiful his situation is even once (unless you're gonna be a Jerkass and say his lash outs at the pureblood who killed his family, or his fits from the pain the transformation and hunger caused him weren't necessary on his part and qualifies him as a wangster.) ...what?
Fuuka from Vampire Knight: Ice Blue no Tsumi. After all, she does end up becoming a Level E vampire and is killed at her personal request.
Unintentionally Unsympathetic: In lines with his Designated Hero status above, the entire final volume makes Kaname out to be a massive Woobie who had good intentions all along and thus everyone should pity him, which may have worked out better had the guy actually shown any remorse at all over his actions. Instead, he's clearly shown grinning over one of his victims at one point, and in the end states that he has "no regrets", whether it's towards his unexplained genocide mission, cruel treatment of Zero or his emotional abuse of Yuuki. Yet, the narrative writes him out like a great person who everyone (even Zero) will revere and remember... because he gave his heart to the hunters' furnace after having chased the former source away for no good reason. What.
Zero gets this too, to an extent, for the fans who feel that some of, or most of his suffering is "self-inflicted."
Values Dissonance: Kaname/Yuuki seem to be the generally favored pairing in asian countries, specially China, where the man playing a dominant and superior role in a relationship is still a common norm. In western countries where equality between men and women is more highly regarded and encouraged, Zero/Yuuki appears more popular.
Viewer Gender Confusion: In the manga, many fans assumed the President of the Hunters Association was a woman, until they watched the anime that is...
At the end, some fans are confused over whether Yuuki's child with Zero is a boy or girl.
Wangst: Yuuki sometimes fall into this in the second arc, frequently complaining over whether or not she's worthy of Kaname or Zero, or that everything bad that happens is ultimately her fault. While she's meant to be a Tragic Heroine, her attitude all too often falls more into being tragic than heroic.