A few quests later and you are sent to get the Twin Alder to find the elder sylph in a quest called Spirited Away
There is a quest called Wretched Hive of Villainy, the questgiver opens by saying the location (a hive) Wasn't initially a "wretched nest of scum and villainy".
There's even a shout out to This Very Wiki! One of the quests is called "Enemy Mine" and it involves someone in the South Shroud (In a city state that doesn't approve of poaching) asking the poachers and Redberry Wasps to look out for Garleans.
The quest to unlock Hard Mode for Tam-Tara Deepcroft is called Corpse Groom.
One guildleve quest in Coerthas is called "We Can Dismember It For You Wholesale", a reference to a Philip K. Dick short story titled "We Can Remember It For You Wholesale", which in turn was the basis for the movie Total Recall.
One vanity pet you can own is a gray cube with legs and wings called the "Demon Brick". It is believed to be a shoutout to World of Warcraft developer Ghostcrawler, who famously expressed his annoyance with theorycrafters by saying they'd use a featureless gray cube for a pet if it gave them a little extra DPS.
One of the attacks used in the final fight for Tam-tara Deepcroft Hard Mode is Red Wedding.
In Hull Breaker Isle, the final boss is a Kraken, who uses an attack called At World's End.
In Ul'dah at "The Platinum Mirage", a Mammet will tell your fortune. After analyzing you, he can tell you "The answer... is 42."
In the Twelveswood surrounding Gridania, there is a type of Galago (monkey-creatures) called "Curious Galago".