The Arrival - S1-E4
Trivia: Michael Cerveris makes his first significant appearance in this episode as The Observer/Bald Man. However if you watch the series from the beginning, he makes fleeting appearances in every episode, sometimes on a tv screen.
Trivia: Cameron meets a prototype robot that smiles and waves at her in in the exhibition outside the chess tournament. Briefly visible on its control screen, alongside basic commands, is the word "BladeRunner", a reference to the classic sci-fi film which also features a dystopian future populated by humanoid robots.
Clone Cadets - S3-E1
Trivia: Commander Colt watches Domino Squad do their test and says, "Start The Citadel challenge, version THX, variable 1138," which is a reference to THX 1138, another film by George Lucas.
The Scorn of the Star Sapphire! - S3-E5
Trivia: After freeing Miss Taylor from the grip of Star Sapphire, Green Lantern encases her in a green energy box and flies her away. The box is shaped almost exactly like a shuttle craft from Star Trek. (00:15:50)
Trivia: After the series became a major success upon release in 2008, director Joss Whedon teased that he would be doing a sort-of "sequel" at some point in the future. At one point, an outline and a number of songs for the sequel were written, though due to other obligations, Whedon had to push back production. As of 2018, the long-rumored sequel has yet to materialize, though everyone involved has continued to hint that a follow-up may still happen eventually.