Subject 19 is given the code name Athena. Alex Mercer was given the code name ZEUS by Blackwatch. Word of God states that it was suppose to be a joke, using another Greek mythological God as Subject 19's code name.
Cobalt Leader's real name is revealed to be Zachary Slavik
The Human Cobalt Soldier's name is Sharon Redfield
Shelton mentions Kepler's Laws of Planetary Motion when describing how Gamas formed.
James uses the Coriolis Effect to select a corridor in Pavlov's Checkmate.
Shelton also mentions having an Erdos number of 7 in the first RP. Which is actually a rather pathetic Erdos number.
The Cobalt Squad in the first RP had a tendency to use famous scientists' names as derogatory terms directed toward the scientist characters, Examples of names used as such include Newton, Hawking, and Bill Nye.
Kerzach is mentioned as having worked on a Small Hadron Collider, which later plays a role in Schrodinger's Prisoners.
Rara Terra Smelting from Fool's Gold by Serris is established as lanthanide refinery.
Rara Terra means "Rare Earth" in Latin. Rare earth is an old name for lanthanides.
Shelton says the Dragonstorm "thought network" was a branch-off of the phone tooth invented in 2002.
A scientist named Dr. Dyson Holmes is the subject of a really long and convoluted shout out. Spoilered below:
"Dy" and "Ho" - the letters for Dysprosium and Holmium.
The lab report he worked on is titled "Toxicity of Lanthanide Containing Alloys In Pediatric Psions" - Dysprosium and Holmium are lanthanides.
There is also a reference to Dr. Holmes being "hard to find". Dysprosium is named after the Greek word "dysprositos (δυσπρόσιτος)", meaning "hard to get".
LB&T's answer works too. He thought "Dyson Holmes" was a reference to Sherlock Holmes and the Dyson Sphere, since both are "hard to find" (Holmes because he's a detective, good at remaining unseen, and Dyson Sphere because 1] they don't exist and 2] a Dyson shell would block the rays of the encompassed sun making it hard to see from an astronomical viewpoint.)
Krebs-Calvin Pharmaceuticals is mentioned in the second RP.
James's favorite expression is allegedly "I'll trust you when there are two electrons with the same spin occupy the same atomic orbital". Spoilered below:
Electrons cannot occupy the same atomic orbital unless their spin quantum numbers are different.
A tiny mining town in Texas is named Platanna Town.
The third RP reveals that a big budget movie is being made about the first terrorist attack. Name-dropped actors include Robert Downey, Jr., Thomas Kretschmann, and Neil Patrick Harris. We also get this exchange:
Shelton: "You could be looking at the next Dave Bowman."
Cobalt Leader: "Hm, the way I remember your role in the whole situation, you'd probably be closer to the Chevron Guy on Stargate."
A shooting range in the 3rd RP is called Czerka Tactical Arena.
It is mentioned that Dr. Stan Lee first discovered the mechanism by which psychic powers work in 1963.
The first psi-experiment created is named Jean Gray and in a Shout-Out to X-Men: The Last Stand she is eventually put down by the scientists after her telekinetic powers went out of control and killed several scientists.
Do note however, that the "telekinetic meltdown" manifested in the form of people getting violently thrown around, not in the form of people and objects getting disintegrated.
A Sgt. Frank Castle is seen as a member of the United States Army
A Chimera-based Dragonstorm experiment attacks Kiara and Hailey in the 3rd RP