Adult Fear: By a non-related character, no less. Trigger Happy, a town guard, is distraught when Puppysmiles runs into a death fortress full of certain death, and rushes to save her. Her fears are realized when she sees several Security Bots cut Puppy to ribbons with machine-gun fire. Puppy gets better, of course.
Attention Deficit... Ooh, Shiny!: Puppysmiles is an easily distracted young foal, and puts pretty much anything that's colorful and small enough to carry into her saddlebags (bits of glass, ammunition, pieces of plastic, whatever). Luckily enough, this is how her suit's repair system is able to still function even after being shot and torn dozens of times over the course of the story; it just uses Puppysmiles' findings as raw material.
Atomic F-Bomb: Molten Gold drops one when Puppy's cluelessness wears out his temper.
Molten Gold: Why a fucking retarded foal, why!? FUUUUUCK!
Black Comedy: Puppy, blissfully ignorant as always, adopts a dead parador cub as a pet and winds up carrying its decomposing carcass with her for several chapters. She remains unfazed by the disgusted reactions of the ponies she meets.
Stretch your definition of 'baby' a little, and Puppy is dead baby comedy.
Deadpan Snarker: Several of the people Puppy meets fit the bill, and even Mister Voice gets in on it occasionally. Probably entirely by accident.
Puppysmiles: Uh... mister Voice, gimme that shiny thing that makes a lot of noise. Mister Voice: Warning. Object Puppysmiles cannot be retrieved from inventory.
Death from Above: Puppysmiles accidentaly designates a Steel Ranger holdout for a Solaris Orbital Artillery strike. The Applejack's Rangers who were assaulting the compund were pleasantly surprised on how quickly the battle ended afterwards.
Demonic Possession: For a brief moment during chapter 12 by what MAY be Nightmare Moon, and then full on at the end in chapter 20 after Puppy learns her mother is dead.
Determinator: Puppysmiles will find her mom, darnit, and she's too busy to let things like death and Post-Apocalyptica get in her way!
Dynamic Entry: Henrietta is prone to these when Puppysmiles wanders off while under her care. Even when the filly is in no danger at all.
Flashback: Puppysmiles frequently has some when something reminds her of certain events in her past.
Footnote Fever: As is customary, Pink Eyes includes a footnote at the end of every chapter describing her level growth.
Foregone Conclusion: Puppysmiles starts out in search of her lost mother Rainy Days. The problem is, it's been two centuries since she last saw her. Unless Rainy Days has been ghoulified or otherwise preserved, her quest is doomed to end in heartbreak. According to Molten Gold, the grave of Rainy Days is located at Emerald Shores, at the of the Big 52, by the sea.
Bittersweet Ending: Rainy Days is long dead, and Puppy's grief at realising her mother is gone forever allows CreepyVoice to take over and kill several of the ponies trying to help her. When Puppy accepts her own death, her body falls apart. However, in the epilogue Puppy and those she inadvertently killed find themselves in the pony afterlife, where Puppy is finally reunited with her parents.
Healing Factor: Being a Canterlot Ghoul, Puppy can survive outrageous injuries. Her list includes being shot, stabbed, dismembered, devoured by a manticore, taking several antimateriel rifles to the chest, and being cut to ribbons by a minigun barrage.
Heroic BSOD: Puppy gets one after accidentally destroying the Steel Ranger's fortress, because she was under the impression that her mother was in there. She gets better once she's told she had moved on already.
Hope Bringer: Puppy, entirely by accident. Her relentless optimism and faith in the inherent goodness of people inspire most of the ponies she meets.
Improbable Weapon User: Puppysmiles' only armnament is a rock. Nothing can stand in her way, especially after she gets several perks that increase its effectiveness.
Incompetence, Inc.: Solaris, Inc., whose fine products included a doorbell with integrated anti-burglary systems that were responsible for electrocuting, among others, dozens of traveling salesponies and several muffin-selling scouts.
Innocent Inaccurate: Being barely above pre-school age, Puppy just can't understand all the horrible things going on around her.
Killer Rabbit: Puppy, though usually by accident. Several of the wasteland nasties that try to kill her discover - much too late - that she's filled with flesh-melting gas.
Mugging the Monster: A random mercenary, hearing tales of the Ghost of 52, decides to put the so-called-legend in her place after she stumbles into him. But she's just a filly who can't even comprehend his threats, and his beatdown consists of spanking her. Eventually, everyone including the mercenary leaves due to the embarassment and awkwardness.
The Nicknamer: Puppysmiles invents nicknames for virtually everything and everyone. Watcher becomes Questioner, Steel Rangers become Robocolts, and a tank shell becomes 'Teapot'.
Undead Child: Of a sort. Puppysmiles is a Canterlot Ghoul and does not qualify as living, but you'd never think of her as anything other than an excited filly if you saw her.
Our Zombies Are Different counts double for Puppy. She's not so much a Canterlot ghoul as she is an ambulatory mass of pink cloud, liquefied flesh and shattered bone, held together by her radsuit, a weak necromantic talisman, and sheer willpower.