The first Visser One, Jara Hamee, Tom (and his Yeerk), all of the auxiliary Animorphs and Rachel from Animorphs. That last one is the impetus of many a Fix Fic. As is the very possible death of all the main group except Cassie.
Commander Root in Artemis Fowl, although he gets a Time Travel cameo in The Time Paradox. Commander Raine Vinyaya also gets it in The Atlantis Complex. Clearly, this is not a good rank for the LEP.
In Firewing, while the villain Goth returns from the dead, Shade ascends to the true afterlife.
In "The Grey Griffins: The Clockwork Chronicles," during the end of the first book, a boy named Robert gets killed, without any chance of coming back, after his spirit's host, a large war robot, is disassembled.
The Dresden Files: The White Council killed Heinrich Kemmler six times and confirmed it, boot on body, every time. Kemmler, being a necromancer of near-divine power, was little more than inconvenienced. When he died the seventh time, after the Council disrupted one of his rituals, it was in no way implausible that he would bounce back that time too. However, Word of God has it that the last time the White Council managed to make it stick, and that Kemmler is finally and permanently dead.
Lots of characters die in fairly straightforward ways in the Harry Potter books but the demise of Sirius Black in Harry Potter and the Order of the Phoenix - knocked through a magic portal during a battle with the Death Eaters - left some wriggle room to bring him back. Nope - no ghost, no magic portrait, no talking diary - he's gone for good.
Guy Gavriel Kay's The Lions of Al-Rassan builds up the hope that when Ammar ibn Khairan and Roderigo Belmonte duel, they will both survive. That is not what happens, and one of them dies (with the other receiving a permanent wound, but otherwise getting a pretty happy ending). Quite a few other characters are permanently killed as well.
A meta-example; defied and averted by Terry Pratchett's editor for Moving Pictures. At the end of the book, he wanted Gaspode and Laddie to stay dead, but his editor urged him to change his decision.
In The Camp Half-Blood Series, multiple characters die and don't stay dead- Jason is charmspoken back to life in The Lost Hero by Piper, Nico lived despite being trapped in the jar without food, water, or air for five days, and Percy and Annabeth come back from Tartarus alive but when Jason Grace dies the second time in The Trials of Apollo, he stays dead.
In the Red Dwarf book Last Human, Rimmer is fatally shot in the light-bee by the alternate Lister. He manages to survive long enough to get Kryten to infect him with the Oblivion Virus, passing it on to The Rage to save the rest of the crew, killing it and himself in the process.
In Warrior Cats, most of the cats who die either end up in StarClan or the Dark Forest, but they're dead all the same and are unable to come back to life, even though some of the dead cats can interact with the living.
Subverted with the leaders, who have nine lives. If they die once, they lose a life, and so on. However, when they lose their last life, they still are killed off for real.
Also subverted with Cinderpelt who gets reincarnated.
Hollyleaf returns in The Forgotten Warrior but was killed off this time in The Last Hope.
Balefire in The Wheel of Time combines this trope with short-term Ret-Gone (the extent of its effects determined by how much power is used). Even the Dark One can't resurrect someone killed by Balefire. However, it can be destabilizing - too much retconning will literally unravel the "threads" of reality.
Most Americans are unaware that Geralt was Killed Off for Real at the end of The Witcher novel series (mainly because only the first book has been translated from Polish). The gameretconned this to an Unexplained Recovery.
Invoked in one of the sideplots of Something Rotten. The author of the wildly popular Emperor Zhark sci-fi series has grown so sick of being asked to write Zhark novels (he originally wrote the novels as a parody of bad sci-fi, but it ended up becoming far more popular than his more serious works), that he has decided to end his latest book by having Emperor Zhark publically executed on-page and explicitly spelling out that he is dead, just to make absolutely sure that nobody can ever ask him to write more Zhark novels.
