In The Gamer's Alliance, a number of heroes and villains, including very prominent ones, have been killed off for real, some more dramatically than others.
A number of main characters in lonelygirl15 have been killed off unexpectedly, including lonelygirl15 herself.
KateModern has unexpectedly killed off a few major recurring characters, often midseries, quite casually, and with bodies shown so that we know they aren't just hiding. It also once killed off a central character offscreen, with no fanfare, as a major plot point.
Although the situation was averted, one of the main characters came very close of dying in the imageboard adventure Ruby Quest. Weaver says he was prepared to kill him off had the players made any harsh decisions. It is likely that such situations might arise once again in the future.
Survival of the Fittest exemplifies this trope, being based off of Battle Royale. Of course, if you really want to get into the nitty gritty aspect of it, it's much more of a Kill 'em All. This is doubly true in that the vast majority of deaths (or at least, when they are to occur) are determined randomly.
Tech Infantry killed off main characters, supporting cast, and Big Bads with abandon. Then came the Y3K Arc, which killed off pretty much every major legend in the TI Universe, before killing off pretty much everyone in the Galaxy.
Normally, this trope is pretty much averted in the Whateley Universe. But it's front and center in the "Loose Cannons" storyline. Of the original twelve teenagers, five are already dead. And the story is only on its second chapter.
Vinny makes it clear in playthrough of Tomodachi Life that he reserves the right to evict any islander he pleases. Most of the less interesting ones suffer, with special mention going to BonziBUDDY and Dolan, who were despised for their memehood and all but stated to have gone to Hell. It gets more a bit more straightforward with the Jahn Army's assimilation plotline, which several well-known islanders succumbed to. While it was partially averted in that the most prominent of the assimilated (Wario) was saved, it still caused Levi, Balegdah, and Jack & Jill, all of average notability, to be lost.
The first chapter of Antlers Colorado makes it very clear that anyone can be killed off, even those listed on the cast page of main characters.