One of the settings - Carceri - is one big STALKERShout-Out, with a heaping of Outlaw Star. The head honcho at the closest thing to a main city there is called Sidorovich. The mysterious "Shipyard X-18" is an installation run by "the government", protected by pirates, and tasked with designing ships that can penetrate deeper into Carceri's deepest layers using a unique navigation system. It even has the Wish Granter as an adventure hook!
In the notes on Dark Eldarin culture, it mentions that they are exceedingly self-aggrandizing, and that they "want all the treasure. All of it!". It is also stated that Dark Eldarin emotional relationships all boil down to either hate or pity.
Also, someone who does poorly in social combat may drop below even normal hostility, into Kissmessitude.
The story at the end of chapter 3 is a reference to a dialogue from the first episode of Slayers.
The excerpt before chapter 9 is a reference to the final episode of Cowboy Bebop.
The "7th Edition" logo on the cover is taken from 7th Sea.
On the more obscure side of references, in possible adventure hooks for the crystal sphere Arcadia, it's mentioned that the farm animals could be positioned to form logic gates and the whole planet might be a computer. This is a double-reference to The Hitchhiker's Guide to the Galaxy, and a legendary thread on /tg/, where somebody suggested that since Necromancers can give their undead creations simple commands, it could be possible to make an undead-powered computer, which posters nicknamed "Deep Rot" (itself a reference to HG2G).
There's a good deal of Mass Effect references throughout the book. The war between Eladrin and Humans is a direct reference to the Relay 314 Incident, Mention of "The Reapers", The Portal Relays, Eladrin pilgrimages, The fall of the Eladrin which details a few things like migrant fleets, the Council. There's probably even more then this.
Dryads have a 3-stage life cycle that references the asari.
The Daemonhost Sin Assets are a reference to the demonic classifications of Dragon Age: Origins.
Edition 1.4 adds a parody of the Library scene from Ghostbusters with a Daemonhost.