* AmbiguouslyEvil: The end of chapter 62 can give that impression [[spoiler: about Natori]]. Some youkai may also be applicable to this.
* CrowningMomentOfHeartwarming: [[Heartwarming/NatsumesBookOfFriends So many that]] making a DrinkingGame out of it would have you unconscious by halfway through the first season.
* DracoInLeatherPants: Matoba Seiji, for obvious reasons.
* EarWorm: The season 3 opening theme.
** This troper found season 2's opening to be this as well
* EnsembleDarkhorse: The black Nyanko-sensei [[spoiler: a god who was trapped in a Maneki-neko, much like Madara, except this one is black]] appears in as much official merchandise as Nyanko-sensei himself (meaning [[SeriesMascot a]] '''[[EverythingsBetterWithPlushies lot]]'''), despite [[OneSceneWonder only appearing once]]. He's also popular in fan art.
** The fox spirit kid is surprisingly popular, and fans of him always say one thing about him: [[RidiculouslyCuteCritter D'AAAAAWWWWWWWW]].
** Gen, the snow bunny-turned-bishounen who, again, appeared in only one episode.
** Hozukigami and Fuzukigami. Or mostly just their [[CoolMask extremely pretty masks]], but it's also common to ship them together.
* FriendlyFandoms: With, of all series, KurokonoBasuke, judging by the multiple crossover fanarts on Pixiv and the fact they aired around the same time. It helps that Natsume and Akashi are both voiced by HiroshiKamiya.
* FoeYay: Part of Matoba's "creepy" vibe involves making plenty of unnecessary physical contact with Natsume. Later, all of his attempts to get Natsume to join the dark si...clan.
* HoYay: So much so it has [[HoYay/NatsumesBookOfFriends its own page]]. It is a shoujo manga afterall.
* PeripheryDemographic: Actually has a sizable male fanbase in spite it being a shoujo.
* SecretSecretKeeper: Shigeru is implied to be have become this thanks to curse incident at his house. He easily brushes off Natsume wrecking the room and does not question it despite Natsume not being able to formulate an explanation behind it. This trait is possibly influenced by the fact that this accident carries much [[FlashBackEcho resemblance to the past]] and that he knows both Natsume and Reiko aren't exactly ordinary people. However, this trope is highly downplayed as he seems to not be completely aware of Natsume's powers.
* TearJerker: This show is ''packed'' with them. The sensitive are advised to watch with a wad of kleenex at the ready.
** And then there was that part in Episode Six [[spoiler: where Natsume cries upon seeing the photograph of the Youkai girl he'd grown attatched to, finally getting to be with the human she had so badly wanted to meet all her life, if only for a few hours before she vanished.]]
** ''Any'' moment where Natsume feels less like an outcast and more like he has a place where he actually belongs doubles as both this and a CMOH.
** The episode with the firefly spirit and her only friend, which had lost the ability to see her. [[GraveOfTheFireflies What is it with anime, fireflies and tear jerkers anyhow?]]
** Episode 4 of Natsume Yuujinchou San, when the youkai haunting a tree drops down to give the revisiting Natsume a gentle hug.
** Episode 5 of the same season when the little youkais watching over the sick Shin'ichiro try to cure him by making their own version of a stethoscope and the little youkai with its hair in a bun sorts of sings to him while shaking the end of the "stethoscope" beside Shin'ichiro's head.
** Every goddamned episode.
* ViewerGenderConfusion: Kogitsune (The Little Fox-child) is still young, is drawn as a [[GenericCuteness generically cute child]], has long, silky hair, and has worn a sun-hat with a pink ribbon and a long, white shirt that could be mistaken for a dress.
* TheWoobie: So. Many. Characters! But particuarly Natsume, in a StoicWoobie fashion.