Stanley Fitzroy brags that his last name means "son of the king," which is literally true. But throughout British history, the connotative meaning of the surname has long been that a person named "Fitzroy" is actually the illegitimate son of the king, and therefore not in line for the throne. Therefore, the name that Stanley is bragging about is actually a symbol of his powerlessness.
Beckman says the Laudenall was taken from box 092407. This is a reference to the air date of the pilot episode of the series, which was September 24, 2007.
Adam Baldwin (John Casey) and Robert Patrick (Col. James Keller) both appeared on The X-files: Per Manum as old colleagues.
First appearance of Caseys daughter, Alex, who was named after his previous incarnation, Alex Coburn.
Regarding the gag where Morgan says the time is 0 twenty two hundred and two p.m.: in military time 1:00 am is 0 one hundred, noon is twelve hundred, 10:02 pm is twenty two hundred two, and way too early in the morning is 0 dark hundred. There are always 4 digits and am or pm is implicit.