At 28 minutes Cassandra mentions how many footsteps it takes for Nathan Fillion to cross the Serenity. These are references to Joss Whedon's "Firefly" series.
Jenkins tells Stone, at the end, how fathers and sons have a very difficult relationship. At the end of Season 1, it's revealed that Jenkins is actually Galahad, son of Lancelot, who was the main antagonist of the first season.
Jenkins says the largest animal in the "Large Animal Room" of the library is Nessie, the Loch Ness Monster, who is often described as a prehistoric reptile known as a plesiosaur. In the earlier film The Librarian III: The Curse of the Judas Chalice (2008), a plesiosaur, presumably Nessie, can be seen swimming in one of the Library pools in the final scene.
Ezekiel proposes a zombie movie marathon, including Dawn of the Dead (1978). Lindy Booth (Cassandra) and Matt Frewer (Dulac in the series' last season) both starred in a remake of Dawn of the Dead (2004).
Just after the Sheriff's vehicle is blown up there is a quick view of the surrounding buildings. One of the images shown is a poster depicting a tree and the label on the poster is "The Tree of Life".