Bokurano: If you lose the game, your universe goes bye-bye. If you win, someone else's goes bye-bye. Provided the tournament has a standard ladder form, 2^15 - 1 universes — 32,767 whole universes, lifeforms included — are destroyed during the anime's tenure. But hey, it may all be for a good reason... Or not.
The standard effects of a Lost Logia reaching full power and going out of control in Magical Girl Lyrical Nanoha are multi-dimensional catastrophes that destroy many worlds in the process.
In Noein, the goal of the title Big Bad is to destroy all possible parallel universes so that only Shangri'La remains.
Crisis on Infinite Earths destroyed almost the entire multiverse and squished the surviving few universes into a messy amalgam universe. Prior to this, the Anti-Monitor destroyed, ultimately, infinity minus five universes.
In JLA/Avengers there was Krona, a being that attempted the destruction of the core universes of both DC and Marvel, in order to remake the new universe that would emerge in his own image.
The plot of Jonathan Hickman's New Avengers is the discovery of a chain-reaction of colliding universes, each one causing the multiverse to contract just a bit more until "everything dies." There are ways to slow the process down, but they are... costly. This ultimately leads in Secret Wars 2015 with all universes destroyed, only bits of them surviving to become Battleworld.
In The Sandman Overture, Glory of the First Circle explains to Morpheus that a star has gone mad and become a cancer in the universe. "From across the vastness of the cosmos, impelled by whatever senses drive them, singular creatures are gathering to feast on the coming massacre and the madness. And the madness will spread. The galaxies themselves will shake and vanish. The other realms in their turn with fade and be destroyed. Soon enough, the mind that is the universe will cease to think, and all things will cease to be."
In Riddle of the Seven Realms by Lyndon Hardy, an ancient demon plots to destroy all known worlds by lighting a fire in his home dimension, which will punch a hole into the void and suck in not only the demon realm, but also all other worlds that connect to it via flames. (Presumably, any undiscovered universes that lack the "flame permeates all" rule of wizardry would escape this fate, making it this level and not Class Z.)
In the 2010 finale of Doctor Who, after the Silence detonates the TARDIS, all that remains of every reality is that of Earth in this universe, just a stone's throw from Class Z. Stars are myths (and our sun is actually the TARDIS burning), all that's left of the Daleks is one shadow in time, and as the characters edge closer to the date of the TARDIS' explosion, people start vanishing from time. This is reset by the Doctor creating a second Big Bang with the Pandorica.
At the end of VVVVVV, you have to destabilize the dimension to get back to your own. However, this has destabilized two dimensions so after the ending you have to find a way to fix them.
Despite Umineko no Naku Koro ni being mostly a romance-mystery novel, in the final battle between Lambdadelta and Bernkastel , both rapid-fire attacks that shatter entire fragments using the force of Big Bangs and Big Crunches. Each fragement is an entire parallel universe. On a (comparitively) lesser scale, Willard cuts an entire fragement in half with a single sword slice.
In Homestuck, Lord English has destroyed (or at least engineered the destruction of) countless universes, including the ones the protagonists are from, and is trying to destroy them all.
It was revealed that when Universes A and B were destroyed by Spades Slick and Jack Noir, respectively, they actually destroyed every possible alternate version of those universes, so it was actually two entire multiverses being destroyed.
At the end of Spider-Man: The Animated Series, Spider-Carnage, an alternate universe Peter Parker who hit the Despair Event Horizon after his universe's version of The Clone Saga and was bonded with the Carnage Symbiote, attempts to destroy the multiverse, aching to a Class Z destruction (although it probably wouldn't count that far, since those sent to stop him are alternate Spider-Men, which probably means only the universes containing or related to Spider-Man would be destroyed).
Similarly, in Turtles Forever Utrom Shredder destroys his native dimension and begins destroying another, eventually wiping out every universe that contains the Teenage Mutant Ninja Turtles.
Nearly happens twice in Danny Phantom; first when the Guys in White try to destroy the Ghost Zone, and again in the finale when Earth is threatened by the "Disasteroid". These apocalypses would have been possible because the Ghost Zone and Earth are opposite dimensions and the destruction of one will destroy the other.