So I recently rewatched Young Justice to help boost the stats for season 3 (if you haven't watched it, or even if you have, I highly recommend! Great watch, even better the second time!), and I noticed considerable amount of similarities between the team and our favorite shinobi.
Shadow Clones Can you say "Ustuj on Nihsnub Egak?" With a little magical assist from Zatanna, Robin pulls off Naruto's signature Shadow Clone Jutsu!
One Armed Characters I could go a couple ways with this one. First, Arsenal here may remind you of a certain Akatsuki member who spent some time missing an arm and also has a thing for blowing shit up. I can't go much into my second direction, as I'm only 152 episodes into Shippuuden, but I have gathered that apparently Sasuke, who, like Roy Harper, doesn't always make the best life choices and is kind of out for himself, also loses an arm, giving them a little more in common.
Transformations While shinobi can use the Transformation Jutsu, the Young Justice team has a few tricks up their sleeve as well, like the charm Nightwing had Zatanna create so that Artemis could infiltrate Black Manta's operation as Tigress. Then there's Miss Martian; as a martian, M'gann has the ability to shapeshift into anyone. She actually always uses this ability, taking the form of a tv show character with a green twist, as she resents her true form because of the oppression of white martians on her home planet. Though she's pretty good at shapeshifting, it's more challenging with boys...
Genjutsu I'd like to see Itachi's genjutsu go up against M'gann's telepathy. After she accidentally hijacked a telepathic training exercise, nearly causing the deaths of the entire team, Martian Manhunter said that Miss Martian's telepathy was stronger than any he had ever encountered. She later uses her abilities to rip information from her enemies' minds, leaving them in a broken, catatonic state. That is until (**SPOILERS**) Kaldur'ahm, believed to be a traitor but actually acting as a double agent, becomes her victim, scaring her straight. She then has to go back into the ruins of his mind to restore him, not an easy task (images 2, 3). She can also transmit images, like when she reveals to Sportsmaster and Jade how Artemis's death was faked (image 4).
Bonus points for voice actors The great Crispin Freeman is the voice actor for Itachi Uchiha in Naruto, and he also voices Roy Harper/Speedy/Red Arrow/Arsenal (gdi that boy has too many names) in Young Justice. And I guess I shouldn't be surprised that Yuri Lowenthal, the voice of Sasuke Uchiha in Naruto, also stars in Young Justice as La'gaan/Lagoon Boy, Aqualad's replacement on the team and M'gann's rebound guy.