All Is Well That Ends Well: When Sasuke came back in time, he murdered the Elders and Danzo by poisoning their tea, then forging a suicide note for Danzo. This...doesn't really have any repercussions. If anything, it made things better because it allows Minato to appoint a much better council.
The Third Hokage's death. While the village undoubtedly mourned his death that day, they eventually moved on. The only side effect is that Kakashi has to deal with accusations of murder from his own team.
The Uchiha Clan Massacre. Sure, the entire clan is dead (again), with the exception of Obito, but thanks to Naruto posing as Orochimaru and having the entire massacre blamed on him, Itachi never has to leave the village and Alternate!Sasuke has had most of his sanity spared...until Future!Sasuke came back and merged with him, taking control over his body.
The actual time traveling. The Team never had any epiphany to actually tell anybody that they were time travelers, because things were going so well, and eventually only confessed when Naruto slipped and used Sage Mode during the Invasion. Even then, they only told Minato, Jiraiya, Tsunade, Itachi, and Anko.
Blatant Lies: Naruto blames the Uchiha massacre on Orochimaru. It works.
Butterfly Effect: The Yondaime Hokage lives, the Sandaime Hokage dies, and Itachi stays in the village. All of this results in Orochimaru still being the Akatsuki which also results with them being a part of the Invasion. This leads to their downfall, and Ame gets a peace agreement with Konoha.
Cutting the Knot: Instead of destroying all of Kakuzu's hearts again, they decide to just take out his brain since he only has one of those.
Running Gag: Several including Naruto's puppet phobia, the list of people Gaara can't kill, Sasuke thinking Sakura is useless, the minimum sanity requirement, and Sasuke being suspected of swearing vengeance against anything that moves.
"You killed the Third Hokage?!"
Serious Business: Team Seven has to pass this Chuunin Exam or they'll be forced to train with Gai.
There Are No Therapists: Subverted. There are plenty of therapists but they're all civilians so most of what the ninjas would need therapists for is classified and the rest would be too much for a civilian to handle.