Final Fantasy 7: Aside form the rather basic possibility of Sephiroth winning at the north crater, meteor impacting and Sephiroth becoming a god by absorbing the lifestream, I could also imagine a timeline where he does not get sent to Nibelheim, never learns the truth and nobody ever gets in a position to successfully oppose Shinra which then rules over the planet with an iron fist while slowly killing it.
Warhammer Fantasy: Chaos wins and gets to destroy reality! Wait a moment...
Puella Magi Madoka Magica: this is more difficult because Homuras time resetting powers make the ending very much dependant on her and her willingness to try again. Maybe she tries so often to get a better timeline that she goes mad or finaly gives up. Madoka, being saddled with all the Karma from Homuras failed attempts makes a pact with Kyubei with a mostly meaningless wish, inevitably becomes a witch at some point and basically ends up destroying the world/universe.
Space Battleship Yamato: Rather easy, the Gamilas destroy the Yamato before it reaches Iscandar and humanity goes extinct.
To get a realy terrible ending you have to have Madoka throw away her power to fundamentally change the universe for something much less consequential, but your idea would make for a much better story, while mine would just end everything right there.
