Ezekiel mentions that there is a department of strange files in the FBI. This is a reference to the TV show The X-Files (1993).
Flynn refers to Ezekiel as a stainless steel rat. Harry Harrison wrote a series of comic science fiction novels about a master thief in a high tech, spacefaring society. That thief was the stainless steel rat.
Stone, heritage site saver, mentions saving the Bamiyan Buddhas from the Taliban. The Bamiyan Buddhas were two 1500 year old statues of Buddha carved from a cliff face. They were 115 and 174 feet tall. In 2001 the ultraconservative Taliban destroyed the statues for reasons of religious intolerance.
The made-up town of Cicely, Washington is actually Forest Grove, Oregon.
When Flynn points out Jake couldn't possibly have the time to simultaneously solve crime, protect World Heritage sites, and run eleven separate college departments, Jake says, "You make time for what's important." This echoes Eliot Spencer from Leverage (2008), another John Rogers and Dean Devlin production. Eliot has a wide range of eclectic and labor-intensive hobbies, and when asked how he finds the time, he says, "You MAKE time". He further claims to sleep only 90 minutes a day. Both characters are played by Christian Kane.