That's less a Captain Obvious and more Sarcasm Mode; he's mocking plot and the extremely trivial social antics of the protagonists in a show that is supposedly an action series about ninjas. On the same level:
Naruto: This expired milk is an important plot point! In a show about NINJAS!
"Nobody will ever understand the pain of being voiced by Yuri Lowenthal, one of the most talented voice actors who ever lived. I am forever doomed to sound like an attractive young man with a wide range of emotions."
Flanderization: Iruka started of as rather eccentric, but still tried to be a competant teacher. His love for One Piece in episode 1 was only mentioned in passing. Episode 2 and onwards, being a One PieceFan Boy seems to be Iruka's only characteristic.
Flat Character: The Princess in The Movie, who only ever says "What-ever!" and barely appears. According to the commentary, this represents a comedic exaggeration of how LittleKuriboh viewed her Living MacGuffin role in the actual film, basically having no relevance to the plot as a character rather than just a plot device.
"Do-do-dododo-dooo! I'm gonna fuck you in the ass!"
Also Joekage's rant.
Joekage: "Personally I don't see what's so important about a bridge. I mean, come on. First one guy makes a bridge. And everybody uses it, they're like, "Ooh, look, a bridge. That's new." So, like, these other two guys make another bridge. And it's kinda like the first one, but people use it anyway because the first guy is like "Oh, their bridge is pretty cool too, check it out." And then these three other guys are like, "Oh, we're going to make the best bridge ever, we're going to combine our talents and be like, 'Oh, look at our bridge, it's totally amazing, ooh.'" and it's like, it turns out really good, and it's the best out of all the other bridges. Everybody subscribes to it."
Naruto: "Subscribes to it?!"
Joekage: "I mean er... Everybody crosses it. Because it's a bridge. Yeah. And before you know it everybody and their mother is making a bridge! So there's a bridge. Everywhere... Nobody even knows why they're making a bridge anymore. They just want people to cross it. They don't care where they're going. The first guy is like, "I'm going to go to conventions to promote my bridge!" It's like, it's just a bridge. It's not a big deal. Get over it."
Naruto: "What's he talking about?"
David Bowie: "Apparently, bridges."
The opening of episode 7, which came out shortly after Masako announced that he was leaving Naruto The Abridged Series. Part of Kakashi/Bowie's dialogue was copied directly from Masako's YouTube announcement.
Bowie: Well, students, it's been a good ride, but I'm afraid I have to leave. There's just too much going on in my personal life. I wanted to say this to your faces, because you're awesome like that. So, farewell. Naruto: Bowie-sensei! You can't leave! We need you! Who else is going to provide all the voices... of reason?
And, come to think of it, a lot of the other dialogue from episode 7 also counts, with all the discussion of building "a bridge" and one guy bringing his girlfriend to help with the bridge and so on.
Leitmotif: Beethoven's Moonlight Sonata plays whenever Sasuke is being emo. Which is always.
No Name Given: A Running Gag with several characters. Iruka is always only known as "The Annoying Sensei Guy" and every other member of Sasuke's family is only described in terms of their relations to him.
Notably, even Sasuke refers to his brother as "Sasuke's Brother".
Sound Effect Bleep: The usual effect applies until Episode 3, when the series becomes uncensored.
Spoof Aesop: "The old man's story has taught me a valuable lesson, and that is that we should not complain about Masako leaving, because we should be grateful for everything that he has done for us and respect his decision to move on with his life." That message is fine, but it had nothing to do with the old man's story.
The Stinger of episode 3 has the Hokage and Kakashi in Naruto's apartment and sets up a joke exactly the same way as in Naruto The Abridged Series by having the Hokage order Kakashi to say something funny about a carton of milk. In the abridged series Kakashi just says "Heh, moo." In the spoof series he does a short parody of Starman.
Half of Episode 7 is a massive one against Vegeta3986note one of the Naruto Abridged creators; the episode was made after his partner MasakoX quit the show and he himself quit Team Four Star, especially his choice to bring his girlfriend onto the show.
MasakoX's odd pronunciation of the word "anything" is heavily lampshaded in Episode 8, in which Sasuke repeatedly pronounces it in an exaggerated manner.
Tempting Fate: After finding out the princess had been kidnapped in the movie.
Kakashi: It's okay everyone. I sent Naruto to go find her. I'm sure they'll be just fine...
cut to Naruto running from a giant train
Naruto: THE POLAR EXPRESS IS TRYING TO KILL MEEEEEE!!
Kakashi: Unless of course they were attacked by some sort of magical ninja train, but that would just be the most retarded plot twist of all oh my God, it is M. Night Shamamalama.
During Zabuza and Bowie's fight in episode 6:
Naruto: Holy shit, this is the manliest thing I've ever seen! This is way more exciting than Dragon Ball Z, where all the characters just stand opposite each other and charge up their attacks— *Zabuza and Bowie stand opposite each other and start performing hand seals* AW, COME ON!
Third-Person Person: A strange variation. While Sasuke refers to himself in the first person just fine, when referring to his family members he often mentions their relation to him in the third person, such as "Sasuke's Brother" or "Sasuke's Father".
Throw It In: Naruto's flubbed lines in episodes 3 and 5. Not known if LittleKuriboh did them on purpose, or just left in his own mistakes. Either way, sure to become a Running Gag.
Naruto: Oh my God, Sasuke is so pucking—pah pah... Oh my God, Sasuke is so fucking pretty!
Naruto: He must be a apbleblahblah. *beat* He must be some kind of optical illusion!
He mentions in the commentary for the movie that accidentally mispronounced "nuclear" as "nucular" while recording and, instead of rerecording, just decided to put a quick subtitle that says "Ninjas can't pronounce nuclear".
Unnamed Parent: In episode 7, Sasuke refers to his father as "Sasuke's father."
Unspoken Plan Guarantee: Referred to by Not-David Bowie as "The ancient ninja art of not telling you what I was doing."
Up to Eleven: In the Swedish dub of the series Naruto's voice is much more raspy than the original. Actually some commenters has pointed out that it sounds like Naruto is dying of lung cancer.
The voice is probably quite painfull for the dubber to perform. It's especially evident in the dub of Spoof Movie no Jutsu when Naruto sings an entire song in that voice. The dubber's voice sounds so exhausted it's easy to feel sorry for the guy.
Utility Magic: Eating food is apparently a jutsu, then again Naruto is a moron so maybe not.
Vocal Evolution: The Naruto voice changes distinctly between the first episode and the second. It can probably be chalked up to his cigarettes.
Sasuke's accent has changed from an American one to a British one. And it sounds almost exactly like LittleKuriboh's speaking tone. Only...emo.
Iruka (the "annoying sensei guy") has become more high-pitched, to the point of sounding like Meowth. This has been lampshaded at least once
David Bowie gradually stops "singing" his dialogue.
Well, not all his dialogue. "Now I'm going to teach you all how to CLIMB A TREEEEE~!"
Ino: Hey, Sakura, Christina Ricci called. She wants her giant forehead back, and her movie career. Sakura: Well, Renee Zellweger called. She wants her UGLY BLONDE BITCH FACE back! ...And her movie career.
And from the movie:
Cliche Henchman 1: Hey, David Bowie, the seventies called, and they want their timely references back! Kakashi: Oh yeah? Well, Advent Children called and they want their crappy villains back!