Sayonara, Zetsubou-Sensei is chock-full of this, particularly when the title character keeps trying to commit suicide in outlandish ways (starting less than a minute into the first episode), and even has a little notebook of students who can commit suicide with him. Not to mention he owns a suicide kit that he'll often offer to other people who he thinks are in despair. Said kit contains numerous methods and devices used to kill oneself, his will, ink and quill for a Suicide Note, and a "BestofEnya" CD.◊
In X1999 Seishiro and Fuuma joke about how they won't be able to enjoy the ice cream from the nice ice cream shop in Shinjuku while watching the Shinjuku area being destroyed.
Cat Soup or Nekojiru-sou was a show that had a reputation for being a combination of cute but dark.
The Kurosagi Corpse Delivery Service, both due to the bizarreness of the setting; the main characters ship corpses around for a living in return for being allowed to loot the corpse's material possessions (and the occasional karmic payoff) by the souls of the deceased, but also from the way they deal with said job.
Stink Bomb, from the Memories trilogy, plays the death of tens of thousands of people and the destruction of Tokyo by a biological weapon for laughs.
Welcome to the NHK certainly was advertised as this and generally works well like this, although it works better as a comedy to some than to others.
The Durarara!! manga features "manga torture" conducted by otaku torture technicians. It involves having the victim selecting a manga, and then they get tortured by a means taken from that work. What truly makes it Black Comedy is how the torturers declare that, really, the content of the manga has absolutely nothing to do with it. They're just twisted people who, if they weren't otaku, would have had other interests — interests that they would be equally good at turning into demented tortures.
Appears occasionally in Paranoia Agent — most noticeably the episode titled "Happy Family Planning", about a group of people trying to kill themselves after making an internet suicide pact.
A few of the games the gang plays in Higurashi: When They Cry counts as this. Once they talked about what they would use if they were to kill someone and how. Another time Mion sent everyone to look for body pieces at the dump. Knowing the series, this is usually foreshadowing or a plot point.
Fire Punch often dips into black comedy, usually through the sometimes ridiculous situations characters find themselves in. However, it's probably for the best, because if not for those moments, the story would be unrelentingly bleak with humanity on its last legs as the world freezes over. Plus all the death, much of which is caused by the main character.
Oruchuban Ebichu was outright designed to push the envelope as to what could be aired in the Japanese late night slot. As said in its entry, Ebichu has a long tendency of interrupting the protagonists in flagrante delicto...
Humanity Has Declined is a bright, happy and cheerful series about humanity dying out through declining birthrates. The unnamed protagonist is resigned to the fact that most of the people she interacts with have had an IQ bypass.
The bulk of the comedy in Zom 100: Bucket List of the Dead is built on the absurdity of enjoying yourself in the middle of the Zombie Apocalypse. Akira and his friends are way happier now than they were in their previous lives slaving away as to meet corporate and societal expectations.
In second case of Q.E.D., Touma is presented with a case of dead debtor in a closed room. All the suspects (who had the key of the room) had motives to kill him. However, in the end, it's revealed that all the suspects (which are related in some ways) thought their loved one was the one who killed the jerk, and so, engaged in Zany Schemes to protect their loved ones. The punchline is that the jerk was killed by accident, which was arranged by the deceased creditor, who wants to protect the suspects, which are her daughter, her daughter's fiance and her loyal butler.
The Voynich Hotel has this in spades. Murder; frequent attempted suicide; the Yakuza, criminals, and all sorts of unsavoury (and sometimes demonic) characters... It makes horrific things horrifically funny!
Gugure! Kokkuri-san has its moments. Notable is Kokkuri putting up a noose in Kohina's backyard when he realizes he has absolutely no friends, or a light producing a rainbow after refracting off of Inugami's arterial spray. And it's all Played for Laughs.
Some of the SD Gundam skits featuring Lalah Sune as a ghost has her appear with a beam saber shoved in her head.
There exists a Dragon Ball Z figure of Yamcha in his trademark dead pose, and a Chiaotzu backpack depicting him about to self-destruct.
In one of the One Piece Q&A segments, a reader asks why there's such a high mortality rate on mothers in the story. Oda responds "Because the opposite of adventure is mother"
In Cyberpunk: Edgerunners, newcomer Julio starts his first job with David's crew full of confidence and boasting about how ready he is. He then spends the majority of the job cowering in fear as the rest of the crew actually handles the combat. After all of the enemies are dead, he suddenly regains his confidence long enough to run straight into a landmine, getting completely atomized into a giant blood stain. The absolute suddenness of it with the situation surrounding it is just as likely to be hilarious as horrifying. In the aftermath, Julio's own family ridicules his death, not surprised in the least that his own foolishness got him killed.
Lint from Rise of the Outlaw Tamer and His S-Rank Cat Girl is constantly and cheerfully reassured by his companions that he can be healed even if he suffers (insert graphic depiction of death or serious injury here) because one of them is a healer who can cast Back from the Dead.
After God: Both the Institute and Gods are pretty nonchalant regarding their operations despite the high death count in the series, with Mood Whiplash and Toilet Humor not being uncommon.
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