Absentee Actor: Blue and Purple Link are completely absent from Episode 6 as it focused on Green and Red, and later Vaati and Dark Link.
A Taste of Power: During the Broken Mirror Arc, the Links encounter Dark Link in "the second to last dungeon", and he shows off his cloning abilities ala Agent Smith. Considering that the Links had just entered the first dungeon, one could say that they time traveled and saw what Dark Link was going to do later.
Green Link: I um, had a close encounter with a wall master. I dodged his attack but, uh, I ended up falling down.
(Red, Blue, and Purple Link see through his lie)
Red Link: That's some excuse.
Be Careful What You Wish For: Red Link irritably remarks after taking the side of Purple Link that he sometimes wishes that he was in Uncle Alfon's shoes. Shortly thereafter, in order to save a severely injured Red's life after he foolishly attacked a Super Cucco, Green Link and the rest are forced to give him the magic milk, and he ends up filling Alfon's shoes nicely in terms of becoming a very drunk oaf.
Berserk Button: Never, EVER mention KFC around Cojiro. You ain't gonna live to regret it if you do.
Also, even if you are one of his allies/shards, don't ever state or even imply that you intend to rape Princess Zelda in front of Green Link, as Green Link ended up getting into a huge fight with Red after the latter, while drunk, stated that, in his words, "Screw the Money! I Want The Princess! *hic* I wanna F-(OBJECTION!!)"
And for Red Link, don't ever get in his way of having sex with Zelda, or tell him to shut up.
Purple Link does not like it when he is referred to as a noob. Or called the Purple Pipsqueak.
Brick Joke / Chekhov's Gun: Red Link threatens to "use [the Armos Boss'] butt as the next Pedestal of Time". A few episodes later, Dark Link inadvertantly wakes up a sleeping drunken Red Link, and at the end of the massive ass-kicking he gets exactly that.
In regards to the latter trope, it was also subverted early on: Green Link managed to get a (broken) magic mirror, and he and his three other counterparts end up going through a lot of misadventures trying to get back to their reality (more specifically, back to the entrance of the first dungeon). After warping back, Red decides to throw away the mirror because he thinks it will do them more harm than good, despite Green's insistence that he intended to get it fixed. Turns out, barring an extensive trading quest that, depending on the experience of the adventurer, would amount to a year or just a few weeks, the magic mirror was the only way to get to the Twilight Realm where Zelda is being held by Vaati. In other words, Red really should have just let Green take it to be fixed.
And then it turns out that fourth task that Oshus needed to have the Links complete was to find the Magic Mirror. And upon finding out that they got rid of it, he forces them to either do the Tower of Hera twenty times or do the Water Temple.
Deliberately "Mistaken" for Gay: In the beginning of Episode 4, Red sided with Purple in regards to eating Cojiro (the super Cucco that Vaati gave them as an incredibly crude joke regarding them "loving cock"). After Green states the finality of finding someone to sell Cojiro to, Red irritably expresses his decision to side with Purple, leading to this hilarious exchange (which, according to the commentary, was penned by Purple's voice actor):
Red Link: Geesh! For the first time in my life I actually stood on Captain Homo's side. It's times like these that I was in my uncle's shoes.
Purple Link:(shocked) Wait...did he just accuse me for being gay? H-HEY! WAIT UP!
Driven to Suicide: Just barely averted in Episode 5, when a drunken Red Link, suffering from depression in regards to a combination of losing against the Super Cucco and his current drunkeness, was sobbing for Uncle Alfon to forgive him before attempting to fall down into a lake, presumably to commit suicide, only for Green Link to stop him, serving as the primary reason why Green Link has to stay behind.
Four-Temperament Ensemble: Green is phlegmatic (being the stalwart leader of the team), Red is choleric (being the outspoken hot-head), Blue is melancholic (being the logical intellectual), and Purple is sanguine (being the childlike/ignorant type).
Frothy Mugs of Water: Apparently Chateau Romani has alcohol in it, seeing as both Uncle Alfon and Red Link get drunk after drinking it.
Getting Crap Past the Radar: When (an extremely drunk) Red Link is severely beating up Dark Link for the latter waking him up abruptly, one of the things shown is Red Link saying "Hey, I learned this in a temple once... Hey, I take this and then I do this..." with Dark Link begging for him not to do so before giving an inhuman, anguished scream. The commentary stated it was a wedgie, but the way it was done, as well as Green, Blue, and Purple Link's horrified and disgusted expressions as well as the former's quip of "Dude, that was so wrong on so many levels..." made it seem as though Red was actually sodomizing Dark Link.
That scene was intended to be a joke, but Youtube couldn't allow it in, thus forcing the creator to spoil the joke by not only giving an exposition in big words stating that the translation had absolutely nothing to do with sex, but even went as far as to post a link to the actual translation in a special Youtube edition video of Episode 2.2
Hammer Space: A drunken and really PO-ed Red summons a hookshot out of nowhere and hook, line, and sinkers Dark Link. It's even lampshaded by Green and Blue:
Red: (reeling in Dark Link) Get over here!
Green: What the...? Where did he get the hookshot?
Blue: How should I know?
Hero Killer: The Super-Saiyan Cucco: Well, kind of, Red actually survived, but was brutally beaten to a pulp, forcing the other Links to give him the milk, with predictable results.
Heroic Bastard: Possibly Zelda, given that her father stated that Zelda was "an accident."
Incredibly Lame Pun: "Dear Link, you love cock. Signed Vaati". Comes in the mail with a rooster. Naturally, Green Link's not exactly happy with that joke.
Also, in Episode 7, after Cojiro flees despite Purple ordering for him to attack Dark Link, Blue Link says "I'm afraid, he's chickened out on us." A Dark Link then Crosses the Line Twice by beating a drumset by going "bam bam, chang!"
Well, besides Zelda using Din's Fire on him when he attempts to have Octoroks rape/molest her if she doesn't tell him about the Links (and after Dark Link tricked him into doing that in the first place, to boot).
Red Link is this as well. Especially when he got drunk.
Left the Background Music On: When Red Link goes through a self-pitying phase (while drunk, mind you), "Untitled" by Simple Plan plays as Green Link tries to comfort him, only to interrupt himself in order to tell Purple Link to cut off the music box.
Mythology Gag: Subrosia is used as the Hyrulean equivalent of Hell, although the word "Hell" has been used on occasion as well.
How Green managed to defeat the Armos bosses was a reference to the Bremen Mask.
Red Link and Blue Link references the difficulty of the Water Temple in Ocarina of Time in Episode 3note At the time the episode was released, the 3DS, not to mention Ocarina of Time 3DS, which lessened the difficulty of the Water Temple by a substantial amount, had not been released yet. (it's also done in a way that's similar to a Noodle Incident).
The dialogue from the Japanese versions of Link and Zelda in Episode 2.2 was taken directly from the A Link to the Past radio drama. On that note, Uncle Alfon's name was taken directly from the same radio drama as well.
The milk was implied to be alcoholic, an implication also made in Majora's Mask, the same game that it came from.
Dark Link remarks nostalgically that he wished that he was the main villain again, referring to his brief stint as the final boss in The Adventure of Link.
Before that, Red Link was beaten to an inch of his life after trying to eat a Super Cucco.
Noodle Incident: Red and Blue Link's reference to Ocarina of Time's Water Temple was written as such:
Red Link: Oh, please. You were as puzzled as you were the time when you were in the Lake Hylia Water Temple.
Green Link: I was not! You're such a liar!
Purple Link: I had a feeling this would happen...
Blue Link: Me too. I guess it was inevitable. Red is right though. The Water Temple was confusing.
Inverted in Episode 7. The events of Red's drunkenness saga ended with the audience aware of it, but Green tells Blue and Purple never to speak of the events again.
Punctuated! For! Emphasis!: Dark Link pulls off a parody of this in Hyrulean context. It was also done to mock the overuse of the trope, as explained in the commentary, which also explains Zelda's line of "My gosh, that was so predictable."
Lampshaded when Blue Link and Purple Link end up watching a Naruto rip-off conversation between Green Link and Red Link:
Purple Link: The fans are gonna kill us!
Blue Link: Maybe if we don't make it too blatant...
Green Link: I'm gonna be a Hokage someday! ...Whatever that means. Believe it!
Blue Link: ...Nevermind, the fans are gonna kill us.
Speaking of Naruto, that particular scene was intended to be a Take That to the Naruto anime's overuse of filler, as Haidouken Dude, the creator of the series, has painful memories of having to wait for something from Naruto that isn't filler.
Also, Indiana Jones made a cameo where he briefly speaks to the Links while running from a boulder, only to be squashed by a Thwomp. In the same scene, when they discover his barely alive body, this exchange is made:
The Starscream: Dark Link to Vaati, as evidenced by his tricking Vaati into being inflicted with Din's Fire via Zelda in an attempt to interrogate her. Let's just say that Dark Link's going to have a huge punishment awaiting him after Vaati drags him back to the Twilight Realm.
Think of the Children!: After Blue and Purple Link attempt to break up Red and Green Link from their fight in the beginning of Episode 7, they try to state that they should think of Zelda as a way to stop themselves from fighting. Unfortunately, that proved to not be the best advice to give either of them, as Green explains that Zelda is the reason why they are fighting at that moment, since earlier the King offered a reward for Zelda's rescue, and Red, in Green's words, "just wants to rape her."
Written-In Absence: Uncle Alfon's voice actor was unavailable for Episode 7, so the plot explained away his absence by stating that he left the house to get himself drunk at Kakariko Village's Milk Bar (an aspect that Blue Link implies is frequent).
You Monster!: Blue says this to Red and Purple when they vote to actually eat Cojiro in Episode 4.