The code/recognition phrase " per fas et nefas" is Latin for "through right or wrong" and is sometimes used to signify a particular rhetorical fallacy where refuting only one of several arguments for a proposition is falsely assumed to refute the entire proposition.
Tuttle references the show "Alias", a show that has similar plots - albeit dealt with a less light-hearted manner - of a spy discovering their family has a history in the spy business. Also shares a plot point of mothers missing or presumed dead.
The safe deposit box Chuck and Gregory Tuttle retrieve is number 407. Guest star Timothy Dalton (Gregory Tuttle) was the fourth James Bond, aka 007.
WILHELM SCREAM: Heard from one of Volkoff's men as Sarah knocks him down the stairs with a flag pole.
Timothy Dalton's character mentions breaking his thumbs as a way of escaping bondage. This technique had already been mentioned on two occasions, first in Chuck Versus the Suburbs and again in Chuck Versus the Ring: Part 2.