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.
Bittersweet Candy Bowl has killed off several of the fancharaters. 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.
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.
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.
In The Order of the Stick, where as a general rule Death Is Cheap, Lord Shojo was attempted to be resurrected, but apparently he refused to come back (in Dungeons & Dragons, resurrection spell only works if the subject is willing to come back). Similarly, Therkla said she wouldn't come back just before she died. Other characters were killed Deader Than Dead, such as Kubota. Miko is a special case: while there is no in-story proof, the author specifically said she won't come back.
We can now add Tsukiko to the list — Redcloak just had her own wights kill her and eat her body, and no body means no resurrection.
And this came within strips of Redcloak having completely wiped out the Resistance (with the exception of Niu, who escapes).
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.