The lethal diseases mentioned as being stored in Cold Station 12 in this episode are references to various (fictional) diseases which have been mentioned on previous Star Trek series, including xenopolycythemia, Anchilles fever, synthococcus novae type A, Rigelian fever, and Telurian plague.
On the surface of Trialas IV, where Soong raised the Augments, there was a large device composed of two long glowing red tubes. This device has been seen in many places on TNG, DS9, and VOY, including, most interestingly, in Doctor Noonian Soong's lab in Datalore (1988). It is also seen in the control room of Cold Station 12, but with blue lights rather than red. The device was first seen in Star Trek II: The Wrath of Khan (1982) on the space laboratory Regula I. Aside from the Star Trek franchise, the device was also featured in Airplane II: The Sequel (1982), where it was seen on the lunar base commanded by William Shatner's character, Buck Murdock.
This episode received an Emmy Award nomination for Outstanding Stunt Coordination by Vince Deadrick Jr..
At one point, it is said that there are a few hundred thousand possible combinations for the hexadecimal password. However, when Lucas finally reveals it, we see on the screen that it is composed of 16 characters, meaning that there were in fact about 18,446,744,073,709,551,616 (about 18.4 quintillion) possibilities.
47-reference: when the Augments enter Cold Station 12 and Dr. Soong accesses the terminal to gasify the personnel in the control hub, the display of the terminal reads "Initiate Protocol 047".