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.
Claude from the Gaiden is the nastiest Contractor in the anime. While most Contractors are simply amoral, Claude is a relentless sadist who enjoys tormenting people by disguising himself as their loved ones to get a rise from them. His ultimate goal to awaken Izanami to commit genocide on his fellow Contractors, solely for the fun involved in it. He compounds this by unleashing Izanami's powers to murder a group of Contractors who simply wanted to live in peace.
From the manga, Flower Of Darkness we have Coach Daisuke Mioka, a perfect example of how Humans Are Bastards in the series. Daisuke is the handsome young coach of an all girls' academy, but is also a serial womanizer and has affairs with his impressionable, starstruck students, making web porn of them. When one of them, Azusa, finds out, Daisuke tries to silence her by convincing her best friend, his cousin, another conquest, to talk to Azusa so he can save the day from a group of his friends who want to rape them. Daisuke mentions to his friends to go ahead, but he'll just be 'a little late' so they can have their fun and later drugs a teacher so he can sleep with her. When Hei is talking the newly empowered Azusa from leaving Daisuke alone, he gloats how happy he made her, and how it's all the fault of women for what he's done and tries to fry Azusa with a stun gun, which enrages the normally taciturn Hei into trying to kill him in cold blood.
The Contractor antagonist of Flower Of Darkness, Harvest serves as an Evil Counterpart to Hei. While Hei embraces his humanity, Harvest considers humans weak and pathetic an offers humans in mental torment his Black Dandelion, the 'Flower of Darkness' to grant them power at the price of murdering their best friend, not mentioning the flower strips the victim of morality and restraints...and he often gives it to the target as well to see who will kill the other first. Harvest's entire motivation is he was once informed he was inferior to the then fully human Hei. Unable to accept it, Harvest opens the Black Dandelion to infect every human in Tokyo, and from there on the rest of the world, to turn humans into amoral monsters like him so he can judge for himself if morality is necessary and there is "nothing within me." Defined his selfishness and narcissism, when the Black Dandelion is stopped, Harvest declares I alone am the future! before using his enhanced powers to attempt to simply obliterate the entire remainder of the planet.
Of course, Suou also has her fans, who thought that she gave the season a fresh approach which it sorely needed, since season 1 all over again (just substituting Amber with Yin/Izanami would have stagnated the plot).
And then you have the people who think that second season did stagnate the plot, and that Suou's spotlight stealing made it even worse.
Daisuke posting web porn of his conquests whilst they remain ignorant of it. With badly blocked out faces. Then hiring a gang to rape Azusa AND Kyouko, with Kyouko as an unwitting accomplice, just so he can "rescue Azusa" or so she can't tell on him.
The callous and horrible way in which Tanya kills her other best friend/crush Nika.
Kiko's very existence serves as a comedy relief element for the series. Other than Mao's nervous sweat-beads, she's the only other character who's frequently prone to over-exaggerated anime emotions, such as Wingding Eyes whenever an opportunity to make money comes around, and Expressive Hair.
One great Kiko moment was when she and a friend were complaining about Adaptation Decay of some unnamed series.
And, after Mao wakes up in Amber's headquarters, he gives a long, dramatic monologue about how contractors always do the logical thing. When he get caught by the others for trying to non-chalantly walk out of the room, he tries to logically respond with a "Meow."
Most of the OVA. It's basically an omake parodying the main series, particularly mocking Hei's Chick Magnet status and the fact that a White Mask of Doom and a change of clothes really shouldn't be that effective of a disguise. Highlights include slightly loopy fangirl Mayu crushing on him due to his "sexy collarbone" and writing him into her yaoi fanfic (which Yin reads), and what is possibly the absolute silliest Reset Button in the history of fiction.
Ho Yay: Episodes 11 and 12. Hei and Nick became close very quickly, spent a whole night watching the stars together (and made plans to go watch them again afterward), and Hei looked really sad and heartbroken after Nick "betrayed" him.
Hei will die. But his soul will choose to go back in time, the time when he was happiest, and he will be at season 1 first episode. Suou who loves Hei wants to be with him too and wants to be in a time when Hei'd love her, but since he already loves Yin she'll go back in time before Hei is born, and become his mother.note This copypasta jokingly places Hei, Suou, and Yin in the roles of three primary characters in the Shadow Hearts series. Said explanation is a note because it's also the ending to the second game.
Moral Event Horizon: If you somehow still harbored any sympathy for Genma, the throwaway comment in the last episode that he was the one who killed Youko and the implications of having raped her prior or even worse; after her death pushes him straight into Complete Monster territory.
In season 2, Genma invokes the trope in hopes that it can apply to him ("Hey, having an unfortunate past can score me some Moe points!"). note That'd probably work better if Hei didn't have the Dark and Troubled Past thing cornered and Amber, Suo, and Yin weren't covering the moe.
Woolseyism: The first two episodes make more sense and fit the tone of the rest of the series quite a bit better in the dub; in particular, they changed Jean's completely-inconsistent-with-everything-else comments about "installing a personality" to something like "Contractors have feelings too" and replaced Mao's inexplicable line about Hei's coat only being bulletproof when he wears it with an excellent Deadpan Snarker moment along the lines of "Hei doesn't just wear that coat as a fashion statement."