Animal Wrongs Group: Though the RSPCD are stated to do good work, they get the wrong idea about Spike and demand he be 'freed'. To their credit, their leader Just Cause realizes Spike is happy in Ponyville after speaking to him.
Anti-Magic: Dragons are naturally magic resistant, although they are not completely immune to it.
Ascended Extra: The green dragon Spike crossed in "Owl's Well That Ends Well", here called "Razorfang".
Berserk Button: Thanks to dragon territoriality, any insult or threat to the ponies Spike holds dear, especially Twilight, is a Berserk Button for him.
Blessed with Suck: Having great strength, claws that can cut rock, the ability to incinerate a field with a gout of flame, and being the size of a few ponies put together would ordinarily be considered a plus; however, these aren't very conducive to living peacefully in Ponyville.
Cerebus Retcon: Some things that happened in the TV series, such as the events of "Owl's Well that Ends Well," take on a more serious bent when cast in the light of them stemming from a dragon's innate territoriality.
There's also the question of where the School got Spike's egg…
Chekhov's Gun: The same rock that started the whole mess in chapter 3 returns in chapter 15 when Spike throws it into Razorfang's throat to win the duel.
Coming of Age Story: The story is primarily about Spike dealing with the difficulties of growing into an adult dragon; with all of the internal, social, and natural conflicts that that entails. Not that growing up is completely without cool perks for Spike…
Does Not Know His Own Strength: One of Spike's biggest issues with growing up; he is far stronger than he's used to being. This complicates such matters as picking up items without slicing/crushing them. This also goes for his fire-breathing.
Big Macintosh apparently suffered from similar issues when he was young which leads him to offering to teach Spike.
Easily Forgiven: Razorfang, who cared about Spike before their duel to the death but tried to go through with it anyway.
Fantastic Racism: A group of ponies fear Spike and think he is nothing but a bloodthirsty monster. The dragon from Everfree Forest has a very low opinion of ponies, and thinks that Spike is less of a dragon because he was raised by them. Mainly because in the past, ponies would hunt dragons. And vice versa.
Freudian Excuse: The leader of the protester ponies Grape Vine grew up hearing horror stories of her great-grandparents being killed in a greed-grown dragon's rampage.
Gene Hunting: Spike does a little of this to discover if he has any living relatives. It's not a happy story.
Generic Graffiti: Somepony vandalizes the library with this towards Spike between chapters 10 and 11
A Glass in the Hand: If somepony startles Spike while he's holding something, said something usually falls to the floor cleanly sliced.
Go for the Eye: In Chapter 16, when Blarney Stone is the only Anti-Dragon rioter that still wants Spike dead, he decides to throw a torch at his eye! Thankfully, Twilight went Mama Bear and stopped it.
How Do I Shot Web?/Centipede's Dilemma: One of Spike's biggest challenges is learning how to fly. When he finally takes his first flight, he makes it clear that no one is to make him think about how he's doing it.
Last Minute Hookup: Applejack's new relationship with Rainbow Dash is briefly mentioned in the epilogue, as well as Twilight's new-found love for Trixie. Ironically, Spike and Huffy's relationship, the only one which is constantly hinted at, is the only one that isn't fulfilled by the story's end.
Mama Bear: Blarney Stone learned the hard way that trying to hurt Spike in front of Twilight is…unwise.
Mood Whiplash: A mild example, but it still counts: After learning about the untimely death of his biological mother and siblings, Twilight tries to cheer Spike up by telling him that his mother thought him important enough to try and defend from the hunters that killed her. He feels better almost immediately. At least until Spike is bombarded with rather scathing hate-mail and a death threat
Most of chapter 10 is pretty light-hearted, in keeping with the spirit of the show. Then a harpoon nearly takes Spike's head off.
In chapter 11 Spike and the Mane 6 are still recovering from the aforementioned harpoon launching, and just as Spike is starting to feel a little better, a stampede of ponies tell him that Razorfang has been spotted in Ponyville's outskirts.
After the duel with Razorfang, everyone is having a great time at the party for Spike, until the leader of the anti-dragon protesters comes running up screaming for Spike to tell him that there's an anti-dragon riot going on in Ponyville.
Mundane Utility: About the only thing Spike plans to use his strength, flight, sharp claws, and fire-breathing for that actually falls into what a dragon would normally do is "protect Ponyville" otherwise he seems to prefer helping lift heavy rocks, unblock streams, help make charcoal, cook, and generally lend a claw where a hoof or horn won't cut it.
Never Mess with Granny: In Chapter 6, Granny Smith makes her feelings about Spike staying in Ponyville very clear, basically saying that anyone who has a beef with Spike staying where he wants will answer to her.
"Now you jest hush-it, you young whippersnapper! If somepony's goin' to go tryin' to take our dragon away, they're goin' to have words with me, y' hear? An' if I want t' go protestin', well there ain't nopony old enough to tell me otherwise! You brought back our ol' stream where mah Toffee proposed hitchin' to me. Yer good to mah kin, mah farm an' mah village. Yer our dragon, an' I'll whip the tarnation outta anypony who says otherwise!"
No True Scotsman: Razorfang frequently berates Spike for not acting like a "true" dragon. The Wyrmstadt ambassador's representative, who isn't even a dragon, also gets in on the act. Spike is quick to point out the Fridge Logic in their stances. The dragon magician sent to oversee the duel in chapter 15 also gets this from Razorfang since he also befriended Unicorn Ponies nearly two thousand years ago.
In the case of said dragon magician, he has an excellent Shut Up, Hannibal! moment when he reminds all present that he is a freaking dragon wizard.
Oh Crap: Grape Vine, the leader of the protesters that wants Spike gone, was (unpleasantly) surprised to learn that there was a Pony/Dragon peace treaty, which rendered her movements moot.
Outside Inside Slur: After finding out that Spike was raised by ponies, Razorfang says "You are no dragon, hatchling. You are nothing but a mammal in a scaled skin."
Parental Substitute: Twilight and to a lesser extent the rest of the Mane Six, who help Spike deal with the social, physical and emotional challenges of his situation. In the epilogue, Razorfang has become this to Huffy and Spike, even after the revelation that Spike's biological father is still alive.
Protectorate: To reconcile his dragon-born greed and territoriality with his upbringing, Spike has decided to make Ponyville and everyone in it his Protectorate. The ponies are his 'hoard'.
Reasonable Authority Figure: The Princesses and the Mayor are naturally this, but a fairly unexpected one is the Magician of Coal Crater.
Serious Business: Names are a big deal to dragons. Razorfang disapproves of Spike giving out his name to everyone, and is shocked that Twilight, a mere pony, was the one who named Spike.
It turns out that the reason why names are such a big deal is because only a dragon's family is supposed to know the name.
Shaming the Mob: Trixie does this to the anti-dragon rioters. Halfway through, it turns into a rant directed more at herself for her treatment of Huffy. This being Ponyville, the speech works almost perfectly.
Shipper on Deck: Spike actively works on getting Fluttershy and Big Macintosh together.
As made clear by the epilogue, Fluttershy and Big Macintosh did ultimately get together, marrying and even having a daughter. Spike is also attempting to set up Rarity with Just Cause. Twilight even lampshades it.
Twilight: Celestia give me patience. Spike the matchmaker.
WAFF: Suffused with heartwarming moments. E.g. Twilight is Spike's sister, for ever and always, and nopony is allowed to say otherwise - not even Twilight.
Wham Episode: At the end of chapter 10 Someone tries to murder Spike. I suppose YMMV, but the event was important enough to be referenced at least once in the remaining chapters.
What the Hell, Hero?: Princess Celestia gives one to Spike in Chapter 5, for not telling her about the duel, which was being held in close proximity to Ponyville.
"You asked about responsibility. Here is some truth: You have a responsibility to me, your Princess, you have a responsibility as a citizen of Equestria, and you have a responsibility towards those that care for you. You have disappointed me greatly, my dragon."
Who Wants to Live Forever?: Spike is not happy about his projected lifespan, although Princess Luna did provide some perspective along an offer of friendship. On the whole mostly averted once Spike decides that by living as long as he will he can keep the memories of his friends alive for their descendants.
"And then you will die, and I will not. And I will endure."