Many of the initial lines in the trailer became this before the game came out, but particularly:
"RAGE QUIT! RAAAAGE QUIIIIIT!"
"Bark like a dog!"Explanation This was Pit's old line when he faced Twinbellows. It was changed in the game to "Old Pit's here to to teach you some new tricks! Now play dead!"
Super Bash SistersExplanation A quick joke made by Palutena in the tutorial, wherein she deliberately misremembers Super Smash Bros. during a conversation with Pit. As mentioned in Hilarious in Hindsight above, the joke came full circle when 3DS/Wii U was revealed to have a cast with an exceptionally larger number of female characters than other titles, one of which is Palutena herself.
Dark Lord Gaol is a girl!Explanation After defeating Dark Lord Gaol, her helmet comes off, revealing a blonde girl underneath the armor. Gaol also looks a lot like Samus Aran (which might be an intended Audience Reaction).
"Hamazing!"Explanation The Catchphrase of Thanatos, the final Underworld commander, who has a new humanoid form this time (and as an in-universe reason for why he now spells his name correctly when the Blind Idiot Translations used to call him Tanatos up until this point as "the H stands for Hamazing").
"Shazammitylam!"Explanation Pyrrhon's Catchphrase, which he utters in chapter 15 when he helps you fight off the Aurum invasion.
"I'm now a level infinity ultra epic supergod-plus!"Explanation Pyrrhon's phrase when he eventually takes over the Aurum.
"Hey look! A(n) [X]" "Hey look! Who cares!"Explanation A snowclone that comes from an exchange between Pit and Hades in Chapter 15, when Pit spots an Exo Tank. Hades is unimpressed, Viridi and Palutena are confused, and Pit's just happy to find a vehicle.
Viridi is Tsundere for Pit.Explanation Viridi starts out as an enemy, actively trying to kill you during her story arc. Then, after you team up with her and Hades against the Aurum and undergo the Time Skip, she temporarily becomes your mission control, trying to be as nice as possible but still berating you as she helps you.
"Komaytos look an awful lot like little Metroids."Explanation A line said by Pit in Chapter 21, which refers to the fact Komaytos do resemble Metroids. Gunpei Yokoi, the creator of the original Metroid game, also created the original Kid Icarus, game on which Komaytos also appeared. It's even acknowledged in that they latch on to Pit and are only weak to certain attacks, namely melee blows. Even the trophy gets in on the fun: "The last Komayto is not in captivity, and Skyworld is not at peace."
Palutena is a good girl.Explanation A reference to the "Sanae is a good girl" meme from Touhou. Fans of both franchises have pointed out Palutena's similarities to Sanae Kochiya, since both have green hair, have taken somewhat questionable decisions, and are associated with divinity (Palutena is a goddess, whereas Sanae descends from one).