Shawn makes numerous references to the Bourne movies. Guest star Franka Potente was in the first two Bourne movies.
Spot the Pineapple: on a filing cabinet at the police station, there is a pineapple shaped pen/pencil holder.
When Nadia meets Strabinsky at the cabin, she assures that Shawn and Gus are ok in German. Strabinsky replies with one word: "Geschlechtskrankheit". This means STD in German.
When Shawn is in the park pretending to read the newspaper, the front page of the paper is the same as the paper is S4 E5 "Shawn Gets the Yips" - with Petrovich's prison release and mugshot on the front page.
The exchange between Shawn and Agent Driggs where they are claiming they can catch the spy in 19 hours, 13 hours, etc and Shawn finally says "Find that spy" is a reference to the classic game show "Name That Tune". Contestants on the show would compete claiming they could name a tune in 5 notes, 4 notes, 3 notes, etc.