Bittersweet Ending/Web Comics

At the end of Brickworld Saga, both big bads have been defeated and all seems to be well, but then Scribe goes missing and the audience finds out that not only has big bad 01 survived yet again, but now he's possessing Scribe!
The "That Which Redeems" Story Arc from Sluggy Freelance ends with the Demonic Invaders being successfully repelled and Torg returning home safely ... but Alt-Zoe died in the process, an event that haunted Torg for quite some time afterwards. In fact, for bittersweetness perfectly encapsulated, take a look at the very last strip of the story arc (not counting the Dimension of Pain epilogue).
Bittersweet Candy Bowl, obviously.
There is a Spyro fancomic named A Bittersweet End (I think).
In No Rest for The Wicked's "A Modest Proposal" arc, killing the wicked witch does not bring back the dead children, the two rescued children know their father abandoned them, and even though they saved Claire, November wonders if she really did any good.