Mandy Patinkin was dressed in warm clothes during the final scenes because he was going to be performing a concert in New York soon after and was afraid of getting sick. The temperature was 22 degrees Fahrenheit (-5 degrees Celsius).
Gideon and Raphael refer to the seven archangels of the Book of Revelation. Revelation chapters 8 and 9 talk about the seven angels with the seven trumpets who bring tribulation to the earth. Raphael quotes Revelation 7:7 where the first angel brings hail and fire mixed with blood.
Tobias Hankel's former drug program sponsor tells Prentiss and JJ that after his wife left him, Hankel's father "went Section 8." Section 8 is a category of discharge from the United States military, used for a service member judged mentally unfit for service, and spoken in slang as a way to indicate that a person is crazy. The term was popularized by its use in the Korean War sitcom M*A*S*H (1972), in which Cpl. Maxwell Q. Klinger regularly wears dresses and other outlandish outfits in an attempt to get a Section 8 discharge.
Bears a strong resemblance to the book and movie Psycho. In both cases, a troubled man is driven to violence by the alternate personality of an oppressive, and very dead, relative. Tobias Hankel's storing of his father's corpse underground is also akin to Norman Bates putting his mother's corpse in the fruit cellar.