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 Raine Vinyaya also gets it in The Atlantis Complex. Clearly, this is not a good rank for the LEP.
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.
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.
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.