Barnacle Jones and Max from 1/0. Notable as most characters get a "ghost point" which effectively makes death cheap. Barnacle Jones dies before this concept is introduced and Max is killed in an accident with a device specifically designed to avoid the ghost point mechanism. Both get back from the dead when the world ends.
Kairi in the first season of Ansem Retort. Word of God says if she ever comes back to life, he's officially run out of ideas.
Awful Hospital: Jay has figured out how to invoke this in a setting where death is usually only slightly more permanent than a paper cut.
Averted; Fern later discovers that she can simply retrieve the remains that Jay has buried and send them in to be restructurated. However, it's implied that the Unexistentializer, were it to be used, would have a much more permanent effect.
Bittersweet Candy Bowl has killed off several of the fan characters. In particular, Carson is abandoned in the basement of an abandoned house after falling through the floor, his "friends" not caring enough to tell anyone what happened to him. Presumably, he starved to death. Kizuna's creator freaked out over the character's presence in the comic and asked the author to remove her, resulting in this.
Ethan in Ctrl+Alt+Del by the hands of an explosion, after one more comic the strip began to change focus.
In Earthsong, "deaths" are usually a Disney Death—while it looks dire for Nanashi to stab someone in the chest, what really happens is that the Siderean element of the sword removes the person's soulstone and returns them to their home planet (although, in certain cases, they may go back to a death anyway). When Beluosus invades Haven, however, Tengu is mortally wounded and asks to die rather than be sent back, a request Nanashi honors. Then Skogul kills Nanashi, and the author makes clear in The Rant that it is dead-dead. The Spinster is also killed. Other deaths include Morgan and Ulkruz, consumed by Beluosus, and the outlying members of Haven's Guard who had their soulstones ripped out of their chests.
Erfworld example: After Wanda gets the Arkenpliers and reveals its powers of 'decryption', Parson hopes that she can decrypt Bogroll, since he died in a Heroic Sacrifice. This hope is quickly squashed when Wanda points out that his remains "were rather thoroughly obliterated."
The character Bush was killed near the end of Exploitation Now! She started off as a minor character but after Cerebus Syndrome set became one of the two protagonists.
Guilded Age: The cultists' monster seems to be able to do this, since we see Rachel's player trying to get the Kingdoms of Arkerra tech support to restore her mysteriously deleted character.
Homestuck appears to be fond of this, though because of how many ways there are to come back, it remains to be seen just who all is gone for good. The trolls used to die with alarming frequency, and both the kids' and trolls' guardians are all officially dead, with the exception of the post-scratch instance of Dad Egbert/Crocker.
On the other hand, the fairly generous afterlife offered by the dream bubbles means that death is little more than a minor inconvenience. Though it still equates to putting them on a bus for all narrative purposes. It turns out, though, that dream bubbles can be destroyed.
Juu from Inhuman. Word of God even stated in the comments for the page "JUU IS DEAD. DEAD. HE IS DEAD. CORPSE. AND HE IS NOT COMING BACK SO DON'T THREATEN TO BEAT ME UP OVER IT."
The Order of the Stick is a Dungeons & Dragons-based comic, so resurrection is fairly easy. Word of God has excluded True Resurrection from affecting the story, though, so you need something left, and D&D resurrection always requires the subject's consent (and, y'know, a divine caster willing and able to cast the spell), so several people are confirmed not to be returning.
Lord Shojo was attempted to be resurrected, but he refused to come back.
Miko is a special case: while there is no in-story proof, the author specifically said she won't come back.
Therkla said she wouldn't come back just before she died.
Redcloak just had her own wights kill Tsukiko and eat her body, and no body means no resurrection.
Malack and Nale are killed within a few panels of each other. The former was reduced to ash and the latter's corpse was disintegrated specifically to keep him from being resurrected. Plus, the way vampires work in the setting, resurrecting "Malack" would bring back a completely different person who died hundreds of years ago, not the character we all know.
Crystal was resurrected once (or to be more precise, made into a sentient golem). Next time she was dumped into lava, making sure she won't come back ever.
While the canon manga left their fate ambiguous, Sailor Moon Cosmos Arc confirmed that the Starlight Senshi, Kakyuu, and any other senshi whose planet was destroyed were not reincarnated when the Galaxy Cauldron rebooted the universe.
Faye MacIntire from Something*Positive dies quietly in her sleep after skipping a day off work to spend with her loving husband, Fred.
The trope itself became a huge component of the last book of Sonichu. After the author changed a fan character into a woman (Simonla Rosechu) and included her in the comic, he was demanded to remove her multiple times. Eventually the author was extorted into believing that he would be sued if he did not remove her and by that time the demand had been upgraded to killing her off on-panel. Simonla is blown up by an exploding toilet.
Dave Kelly was very fond of this trope in his comics. In Purple Pussy he killed off Shelly Squirrel, and all the characters expected she'd come back since this was just a comic. She didn't. And in his other comic, Living In Grey Town, he had so many important characters killed off willy-nilly that he added in a counter for every time a character died. By the end there were only a handful left.