Naruto has tons of Peggy Sue fics. Those who usually end up going back are the members of Team 7 (including Kakashi) and Shikamaru, sometimes individually, sometimes together. The reason for going back usually has something to do with some event that ended well in canon ended catastrophically instead, causing a Bad Future where the time traveler has nothing left to lose by going back. The event varies, but recent ones make it the Fourth Great Shinobi War, wherein Madara and/or Tobi/Obito won. They also commonly ignore Princess Kaguya's involvement.
A lot of fics in which the genin teams are different, either because someone else is teaching Team 7 or someone else wanted Naruto (such as, for example, Team 8), which shuffled the teams around (these fics are most often Naruto/Hinata). A recurring theme in these is the perception that Kakashi in canon is a terrible teacher and Naruto could be so much stronger if he were trained "properly" (and usually made to wear clothes that aren't orange, despite Naruto's choice of clothing never being treated as an issue in canon).
The in/famous Clan Restoration Act, where one male character is forced/ or wants to pair with multiple women to revive his clan.
Also there multiple fics when Naruto gains an awesome power and virtually every girl except (in most cases) Sakura, usually fall for him that includes his mother, Tsunade and girls he never met like Yugito.
Nearly every story starts with Naruto being hated and attacked by the citizens of Konoha and the Third doing absolutely nothing about it or is too late.
He is sometimes saved by a crossover character or an OC.
Also there are many fics that deal with Naruto bringing back Sasuke only to be betrayed by Sakura and is later exiled/executed by the elders and the "civilian council".
It usually ends up with Naruto gaining Combo Platter Powers, becoming the leader of a village while Konoha gets destroyed economically and loses their allies as well. With war between Orochimaru, Kumo and Iwa.
Twelve-plus young characters of the same age, with a variety of personalities? Let's put them in high school!
Another really common one is the non-massacre AU, usually used as an excuse to pair Itachi and Sakura up.
Fanfics where Naruto turns out to be the last survivor of a made up clannote Usually the Namikaze and gets a new bloodline (particularly the Rinnegan) or Kurama some unexplained way gives alters his genes giving him the bloodline. Before the Uzumaki Clan was revealed in canon but Naruto still doesn't have a bloodline.
Wouldn't the fact that all Uzumaki possess pretty much the same physical attributes count as a bloodline? Kushina flat-out says that the Uzumaki were famous for their massive chakra levels, almost endless stamina and inherent skills in fuinjutsu.
There's also the always popular "Naruto turns against Leaf and gets revenge on everyone that abused him". Or, more accurately, "Naruto turns against Leaf and kills the characters that the author doesn't like and spares the characters the author likes."
Another very popular is NaruHina shippers making Naruto as dumb as possible and having constantly mocked by everyone for not noticing Hinata's feelings. Hinata, herself is usually portrayed as a stuttering like crazy for two seconds before fainting.
Sakura is also portrayed as a screeching harpy and Sasuke's loyal groupie. This has some canonical basis as in the early days Sakura would yell at Naruto for insulting Sasuke, but because a number of fans hate her, this gets taken Up to Eleven in fanfics.
There's also the ever popular de-aged fic, which typically involves a jutsu going wrong and the main character of the story being turned into a child version of him or herself.
A lot of crossovers usually start with the Naruto and Sasuke fighting at Valley of the end and the Kyuubi's and the Curse Seal's chakara will merge and create a portal taking Naruto to a new world.
Usually as an excuse to make Naruto "Better" are plots that go "what if Naruto was 'realistic?note realistic in this case often meaning turning Konoha into a military dictatorship, or some other bizarre alteration to canon'"
Conversely, stories where he actually loves his daughters very much but has to put up a front of aloofness to protect them from the Hyuuga council who can and will do whatever they can to "ensure the safety of the clan" (usually meaning "make sure we make things go our way and keep the Branch family under our thumbs").
Fics where Hinata is in danger of getting the Curse Mark are everywhere despite the fact either sister getting the mark isn't even implied in the series. Expect every Hyuuga but Neji to be evil and abusive to Hinata, including Hanabi who ironically adores Hinata in canon.
The Uzumaki clan turns out to have survived the Iwa and Kumo attack.
Naruto snaps and become a cold-blooded killer.
Crossovers usually make it so outside the Elemental Nations is a part of the world of whichever series the author may choose which will be referred as 'outside the veil'.
A lot of crossovers mostly The DCU have Naruto be a Demon and a cult dedicated to him will awake him and he'll often be a villain.
Superhero crossovers will have Naruto be an antihero who'll kill villainsnote Even though he doesn't believe in killing either and some crossovers may take place after he fought Pain and established his no killing rule and will berate certain heroes for not killing.note Mainly because the author wants them to despite the fact most heroes will usually have grounded reasons for not killing.
Though it's worth noting that quite a few examples use an alternate backstory for Naruto (being trained and joining ANBU, for example) that led to him not developing his canon moral code or have him come really close to crossing the Despair Event Horizon at some point in the series and changing because of that.
Minato and Kushina survives the Kyubi attack and has another child. They later focuses all their attention on the child completely neglectingNaruto in the process..
For some reason the other child will usually be a girl.
There are very few fics that had Minato and Kushina loving both Naruto and the younger child equally. If they did survive. The neglect is rather baffling because Kushina and Minato are actually loving parents who will love their child equally and this can be made into an Irony as Kushina canonically wishes to have a big happy family...
There are many fics with Sakura having just about every Naruto guy under the age of 30 fall in love with her and it's pretty popular to top this off with AU as well.
Some will have it that Kurama invented the Sharigan mostly just so Naruto can get it.
The reason Kurama attacked Konoha is someone (usually Orochimaru) wearing Konoha headband killed his (or depending on the story her) cubs used to be common in the early days. This became obsolete when the real cause of Kurama's attack on Konoha was established.
Not necessarily a huge part of a story but when Naruto meets someone there may be a debate if Naruto's name stands for 'fishcake' or 'maelstrom'.
Danzo kidnaps Naruto and wipes his memories clean turning him into a Wild Child in the process.
Kurama mentors Naruto, calls him "Kit," and helps him learn assorted cool demon powers.
While not always the main plot of a fanfic, some fanfics have Naruto decide Sasuke is beyond redemption and kill him or capture him and leave him to his punishment. These are often done by people who dislike Sasuke and/or the idea of Naruto continuing to try to bring him back after all he's done.
Back in the early days of the Naruto fandom, "Naruto retakes the Chunin Exams" fics use to be common. Then canon trudged on and Naruto became so powerful that pitting him against genin wouldn't be very interesting outside of making it a Crack Fic, causing the idea to become obsolete. Ironically, this plot was used in an OVA where they fix the problem of him being too strong by making rules specifically barring anyone from using senjutsu to make it fair, even though the exams are specifically geared to reward those who cheat and use every advantage they have. Of course he breaks the rule and is disqualified from the exam.
Fanfics where either the Konoha 12 as adults, or their children (usually Boruto or Sarada), are transported into the past have been popping up since the manga ended. Most have them go back to the pre-timeskip, usually pre-Chunin Exam days.
The topic of Child Soldiers don't come up much despite the series revolving around it. Many fanfics go about what making middle and high school aged kids soldiers can do to their psych and general world view. The "First Kill" and "First Time Seeing A Teammate Die" plots are ever popular.
Boruto, Himawari, or Sarada meeting the ghosts of their grandparents. The ghost of Neji are also common in Boruto's and Himawari's cases.
Naruto teaching Hinata how to use Shadow Clones and/or the Rasengan.
The Hyuuga Clan either being central to the main plot, or being the focus of a subplot.
Related to the above, Neji and/or Hanabi being important characters to the story.
As opposed to the above, the Uchiha and the Senju clans not being relevant to the plot, not even in stories in which Sasuke is a main character.
The Byakugan having an evolution/upgrade akin to the Mangekyo Sharingan. Usually, Hinata will be the first one (and sometimes the only one) to awaken this new doujutsu.
Hiashi opposing Naruto and Hinata's relationship. If Hiashi is given a more sympathetic characterization than usual, this role will usually go to some unnamed clan elder(s).
A Love Triangle between Naruto, Hinata and an incredibly transparent Romantic False Lead, who's usually Kiba or Sakura, and on rare instances Shino. Sometimes it can be an OC.
A sometimes seen one takes place after the Sound/Sand invasion where the Sand Council decides that this shinobi that beat Garaa (IE; Naruto) could become quite powerful someday and getting ties to him would benefit them. So let's send a marriage proposal to the Leaf about hitching him to Temari!
Just like many authors use fics to point out their perceived impression of Kakashi being an awful teacher (see above), there are just as many who do the same with the Ninja Academy. It's very common fanfics in which a Jonin-sensei tests a team of newly minted Genin, finds that they're much weaker and ill-prepared to be a ninja than expected, asks them what did they learn at the Academy, and gets shocked upon finding how much the standards decayed since the Jonin was an Academy student. This may or may not end in finding out that a spy has been trying to sabotage Konoha's future generations of ninjas by quietly lowering the Academy standards.