Exalted. In second edition, the Sidereal Martial Art Obsidian Shards of Infinity Style actually has a charm that allows you to choose a bittersweet ending, forcing fate (i. e. the storyteller) to resolve the conflict in one of several different ways.
Battle for Macragge: Hive Fleet Behemoth was stopped...After it consumed hundreds of world, killed billions of people, and completely wiped out Ultramarines 1st company(1/10 of their fighting force). And it was only a scouting party.
That's just in the numeric sense. First Companies tend to hold the veterans and elites of the Chapter. An entire Company, the Tenth, is also composed of pre-Space Marine stage Scouts.
Behemoth wasn't really a scouting party, just the first of many.
Another Tyranid example would be the battle between Hive Fleet Kraken and the Eldar of Craftworld Iyanden. The Craftworld survived and Kraken was destroyed, but by the end, four-fifths of the population were dead note at least in the traditional sense: thanks to their soulstones, Death Is Cheap for the Eldar, and Prince Yriel was bound to the dreaded Spear of Twilight.
Promethean: The Created: You have spent years, perhaps centuries, as a reanimated collection of dead flesh. You've struggled to fulfill your Pilgrimage, created another of your kind, fought off the Pandorans, and fled from the hatred of humanity. Your reward? You lose all of the mighty powers you had, your durability and your strength. You are frail, weak, vulnerable. Your memories may very well evaporate. You still have to live in the World of Darkness, which is just as much of a Crapsack World as it sounds like, and now you have no defense against it. You are human. You have a soul. Your journey is complete.
Vampire: The Masquerade ends this way in the fourth Gehenna scenario, "Crucible of God". Basically, a Class 2 apocalypse has taken place: civilization has been pulverized by the war between humans and vampires and the rise of the Antediluvians that followed; the environment has also suffered considerable damage- particularly during the Lasombra Antediluvian's reign of terror. Outside the relative safety of human settlements, the wilderness is swarming with bands of murderous psychopaths created during Malkav's reign, along with giant ghoul animals bred by Absimiliard, and hideous mutantscrafted by Tzimisce. On the upside, with your help, Saulot has been able to call down the wrath of God on Tzimisce and bring an end to the Curse of Caine; the few Antediluvians that managed to survive Gehenna and ascend into godhood are benevolent enough to leave humanity alone; and though you've lost your immortality and your powers, you're no longer troubled by the Beast or hunger for blood, and you can help rebuild human society with a clean slate.
The second optional ending to the scenario involves you remaining a vampire; in part because God has decided to keep Caine suffering a little longer, you've been transformed into a second-generation vampire, and given the option of creating a new Kindred society alongside the emerging human nations. Still pretty gloomy, but at least you've got power on your side.
In Werewolf: The Apocalypse, even the Time of Judgment scenarios that don't involve a Wyrm victory are still bittersweet.
In the Ragnarok scenario in which the Wyld is victor, the Weaver and Wyrm have been stopped, but the human race and the changing breeds have been completely annihilated, and Gaia will still take centuries to heal.
In the Ragnarok scenario in which the Weaver is victor (and smart enough not to sever the physical world and Umbra), the human race survives, but majesty and creativity leave the world. A mundane, clockwork world is all that remains.
In a scenario in which both the Wyrm and Ananasa escape their respective prisons, the two restore the fabric of reality to balance. Ananasa reweaves the cosmos in such a way as to eliminate the changing breeds and reduce some of Gaia's majesty.
In a scenario in which the Perfect Metis is sacrificed as a scion to the Defiler Wyrm, the player characters must rescue his tormented spirit from the Atrocity Realm and cleanse it in the silver lake of Erebus. The Perfect Metis dies, but his soul is finally at peace. To boot, this cleansing averts the Apocalypse by forcing the Defiler to retreat into the Deep Umbra.
Dungeons & Dragons; this is likely the best ending the Player Characters can hope for in the apocalyptic scenarios presented in the Elder Evils Splat book. The PCs may manage to defeat the beast and Save The World, but given how each Elder Evil comes with a Sign that causes global cataclysms, there may not be much of the world left at that point. (The book does say they are meant to be used as finales for long-running campaigns.) For example, Atropus causes a worldwide zombie plague that causes undead to outnumber the living at worst, the Hulks of Zoretha cause a Hate Plague that causes mortal beings to become enraged and fight each other, and Father Lymic freezes the world with endless night, destroying crops and wildlife and making any recovery a difficult task. What's more, two of them, Pandorym and Zargon, are not truly defeated, and the PCs must do something else to ensure that later.