Dr. Rex, Baron Typhonus, and the Mutant Dinos were finally defeated, but at the cost of the lives of Rex, General, Semick, and many others. However, a lot of emphasis is put on the "sweet" aspect of "bittersweet", such as it being said that their deaths should not be mourned but instead celebrated, to prevent this from sounding like a Downer Ending.
The resolution of the Wallace Bishop side plot is that, despite cutting out the part of his brain that should contain his memories, Wallace still remembers his love for his family. Aww, so sweet, right? But don't forget that Wallace Bishop is still unfit for society and must remain in Napoleon XIV Mental Institution for the rest of his life. That's... rather bitter.
Aside from the final post focused on Angel Eyes and Clint Wayne (who have bonded together to the point they are a ruthless duo in Gold City), many of Atton Rand's last posts deliberately tried to focus on the darker elements but as a compromise retained some degree of hope.
Montoya goes home to his wife and promises a better life for his kids, but he could very easily come down with PTSD.
Sarah Bishop manages to survive the war with her daughter and is reunited with her daughter's biological father, but she is riddled with guilt over her actions and consequently suffering from insomni. Her daughter meanwhile has a severe case of PTSD and a drug addiction, but now the family has a loving husband and father in Pierce who is very clearly determined to help them.
Our Avatars Were In A Room Together The Continuation: The bloody war with the Gears ends and Alpha, Karkat, Solaire and Jekyll/Hyde are returned to normal. However, Fen, still a Gear and facing some serious guilt for her actions, runs off deeper into the Guilty Gear world and is nowhere to be found. Aven, determined to find her, manages to strike a deal with one Rachel Alucard, who projects a personal portal to the Guilty Gear world into the room.
The fates of some of the J-Team members that survived the Draconic Uprising in PMD-B match this. The PEFE Founders for instance end up dying of old age unable to change things back, but they do end up laying the seeds to create a timeline fork and manage to raise families of their own.
The Fallout miniarc ends much like the original game, with the Super Mutants being defeated, but the Vault Dweller being cast out.
Wolf-B ends up saving AU!DS' life through sending a message through the Adamant Orb... at the cost of his own life.
The Orre arc ends with Cipher crushed (at least in Orre), but most of the Admins manage to escape justice (though not defeat), a lot of the J-Team members are left with issues, and Siren/Taylor ends up getting killed shortly after undergoing a Heel-Face Turn. On the other hand, Psyche does manage to conquer her own psychological issues.
In We Are Our Avatars, there is the Witches Game arc; on the one hand, the trolls can't bother the main characters anymore, but on the other, Featherine can. Not to mention Victoria Grayson dies. Granted, she got better, but...