The STN in STN-J stands for "Solomon Toukatsu Nin'idantai", which roughly translates to "Solomon Control Center". The J stands for Japan.
Researchers believe that many people suffering from multiple personality disorder (like Chie in Episode 6: Raindrops) and schizophrenia were mistakenly believed to be witches in the Middle Ages.
The idea of the Confraria, as Methuselah uses it (as a group of church officials that went and persecuted witches), refers back to the Spanish Inquisition. (Episode 12: Precious Illusions)
The rune that appears when Minori is making her mud dumpling is the "Ingwaz" rune. It's named after Ing, who in Norse mythology was consort to Nerthus (Mother Earth). (Episode 17: Dilemma)
Robin asks Nagira why he's helping Amon if their ideologies are so different. In the Japanese version Nagira uses the word "Kasare'en" to describe the relationship. There is no similar English term, but it basically means an "undesirable, yet unseverable relationship or karmic bond."