Not listing repeats here, and this is just off the top of my head - I can imagine I'd find some more if I dig a little harder.
Note - the Gangnam Style reference is only in the story quests related to that NPC, so it's a large 'if you hurry and close the quest windows, you'll miss it' matter.
Some boss items:
(Uncharted Cave, Ulysses's Torture Tools) "They can transform a sane person into a raving maniac in a matter of moments, much like a political debate on Facebook."
Secretary Waver was once an adventurer like you until he took an arrow to the knee. (You need to read the window AFTER making an Eden Crystal)
GG Bank Never will tell you about how it's the only bank in the world founded by leprechauns and built out of reinforced double rainbows.
Mine Garrison Lead Akafon, in addition to Gangnam Style... '"Hey, newbie, if you stay here, we'll party all day and night. It'll be smashing, baby!" Akafon's Austin Powers reference was both horrible and outdated.' This is also story-quest only.
Luscious Kimono series: "This kimono was made for flouncing, that's just what it'll do, and one of these days this kimono is gonna flounce all over you
. That didn't make as much sense as I thought it would..."
The Everyday Uniform Dress series strikes a resemblance to the outfit worn by Vocaloid Miku Hatsune
- the male's Everyday Uniform series, very similar to this image in the video, of a commonly accepted Miku Hatsune genderbend
(maybe not the voice, but for the appearance moreso)
The TVtropes page
for Eden Eternal has some more, too, that haven't been listed here (though quite a few of them listed here, are listed there)