I mentioned Sewell looking like Stabler from SVU already, but Viruscarrier at SHHF noticed that:
In one of the police reports about the abduction of Murphy's son, the officer is listed as a Mr. Elliot Benson. This is a reference to two police officers from Law and Order: SVU Elliot Stabler + Olivia Benson = Elliot Benson.
dig site #7 contains Aglaophotis. I saw a few of HC's halos around the game and on the bell puzzle as well.
On the mirror, mirror sidequest the woman claims to see "people in the mirror" and be mental about it, as well it involved manipulating the room's objects to match the mirror's to complete. This is very much like Origins with Helen and Travis.
The posters in the movie theartre, one is from SM, and a few say Vatra on it. One talks about a popular director from the Czech Republic.
I'm probably not the first to notice but one thing that I noticed with may just be coincidence but when you first enter the otherworld and you walk to the rocking chair and the old stereo, the song called "born free" is I believe the same song used in the first season of Dexter.