Awakening the Sleeping Giant: What Madara unintentionally does in the backstory, just by being his usual manipulative self. Turns out that trying to use genjutsu-based mind control on an actual kitsune (and not the Kyuubi) wasn't the smartest idea.
Badass Family: The entire Namikaze-Uzumaki mini-clan, which happens to include all of their adopted kids too. Their family is widely considered one of the most dangerous groups in the world, even including organizations such as Akatsuki and Oto.
Similarly, the extended clan led by Sesshoumaru is this trope scaled up even further, though the youngest ones are still growing into it.
Battle Couple: Minato and Kushina, even more so than in canon since they actually get the opportunity to show off their combined skills. Which is what finally undoes Madara.
Black Sheep: Obito, to the point of getting kicked out of the Uchiha clan.
Butterfly of Doom: Only crops up once, when the Kumo ambassador's attempt to kidnap Hinata goes a little differently. He gets caught red-handed by Obito, Nariko, and Kakashi, and handed over to Ibiki. Minato, meanwhile, refuses to be cowed by the Raikage and relations between Kumo and Konoha are a little...strained.
Creator Cameo: One of the three members of an all-kunoichi team helping to proctor the Chuunin Exams.
Curb-Stomp Battle: Whenever Minato gets within three feet of a fight. There's a reason he's the Yondaime Hokage after all. The fight with Madara is the only time this is averted.
A specific example of this is Minato's rescue of his team during the mission where Obito would have died in canon. It takes him less than ten seconds to kill the entire attack force.
Also, Team Seven's bell test fight is hilariously one-sided in Kakashi's favor, as usual.
Fix Fic: It was started because Obito is the author's favorite character.
Flat "What.": Kakashi's basic reaction to the insanity when he's a teenager.
In Spite of a Nail: Iruka's parents still die, just under different circumstances. Madara still attacks Konoha. The Uchiha clan dies, just eight years ahead of schedule. The Kumo ambassador still tries to kidnap Hinata. Iwa and Konoha still don't get along.
Japanese Mythology: A prominent part of the backstory, given that the InuYasha cast is pretty much a living representation of many of the youkai involved. Oddly enough, only Momo (out of the kitsune seen so far) has a hoshi no tama. In Konoha, Nariko functions as the local loremaster.
Kitsune: The fox clan, who very pointedly do not count the Kyuubi as an actual fox.
Magic A Is Magic A: Chakra is the primary type, and the most versatile. Bijuu chakra is still considered chakra, just too intense for humans to handle. Then there's reiki, which is the exclusive domain of Kagome since she's the only miko in the entire story. Finally, youki, which is the energy type used by youkai of all types. The latter is extremely dangerous to humans with chakra—the mix seems to make youki even more intense. Reiki, meanwhile, blows right through most youki.
Also, ninjas have to train themselves to detect youki, but they can't sense reiki at all. Youkai lack chakra coils, but the effects of youki attacks can occasionally be mistaken for extremely powerful ninjutsu by an inexperienced observer. The only real difference to a layman is that youki never requires hand seals.
Mayfly-December Romance: Brought up regarding most of the InuYasha couples, aside from Shippou and Souten, since both Kagome and Rin are human with inexplicably long lifespans. Nariko gives this as her reason that she won't pursue a relationship with a human, since she has no workaround.
Mood Whiplash: Chapters six and seven relative to the rest of the story.
The Nicknamer: Obito, at least with people he doesn't like. This led to him called Kisame "Sushi" and Orochimaru "Chalky."
Nariko eventually picks up the habit from him, and decides to read other characters' names literally. So, Kakashi is "Scarecrow" to her.
No Sell: Kitsune youkai are entirely immune to genjutsu, which screws Madara over in the backstory. Likewise, inu youkai like Amaya and Sanyu are immune to/can attack freely despite Madara's space-time manipulation. This is because of the use of the dimension-slicing Meidou Zangetsuha from the InuYasha series and the traits being passed down.
Noodle Incident: How Iruka passed his Chuunin Exam, how Obito got that one nickname, and why Kakashi has a fanclub.
The Promise: What started it all. Once upon a time, Souten promised Sakumo that her family would look after his in a time of need. Unfortunately, he died before she could fulfill it. It fell to Nariko nearly ten years later. Foxes, after all, can't break their word.
The Red Baron: Lots of the characters picked up nicknames over the years. These are just the non-canon ones.
Red Right Hand: Momo has a fox-shaped shadow that gives away her human disguises.
Running Gag: Nariko getting stabbed all the time and generally being a dead weight in a fight, Kushina pranking people almost at random, Kakashi being chased by fangirls, and Souten popping up every few chapters as though to remind people that she's still alive.
Spanner in the Works: Amaya, Umeko, and Haruki were all on-site when Naruto was born. This completely throws off Madara's plan to kidnap the infant Naruto and forces him to attack Konoha without the Kyuubi. It didn't go well for him.
The Stations of the Canon: The Wave mission still happens, as will the Chuunin Exam invasion. However, as a result of a lot of changed backstory and characters interfering with each other from both canons, the specifics are going to be quite a bit different.
Summon Magic: In addition to the canon contracts, there are a few more.
Terms of Endangerment: Inverted with Nariko, who will refer to nearly everyone with "-chan," even villains and people she doesn't like. She reserves "-sama" for people she respects more than all others. Meanwhile, Orochimaru keeps his old habit of referring to Sasuke as "Sasuke-kun."
Team Sakumo: Sakumo (crops), Kuwa (hoe), and Kama (scythe).
Team Obito: Akai (red), Hakuto (white), and Momoiro (pink).
Team Takomi: Takomi (octopus), Mizuki (water), Koi (fish), and Iruka (dolphin).
Time Abyss: One of Sesshoumaru's features. He's been alive for so long that most people just do not have any clue what it actually means. This is mainly because the shinobi countries don't have the same scale of history that the youkai characters are used to. They think a three hundred is a pretty long time for a village to be around, since their world is so violent and ever-changing.