The first episode in which Chuck uses the "Charles Carmichael" alias.
Morgan states that Chuck is 6' 1". Zachary Levi is actually 6' 3".
When Morgan is locked in the cage at work, the classical music playing is the same that Andy Dufresne played in The Shawshank Redemption (1994) in the yard.
Morgan calls Chuck a gelding when what he in fact means is a Gelfling, an elf-like creature from Jim Henson's 1982 puppet fantasy film The Dark Crystal (1982). A gelding is a castrated domesticated animal, especially a horse.
Matthew Willing's (Uri) first appearance in Chuck. He comes back in season 4 (Chuck versus the Gobbler) as Yuri the Gobbler.