A pirate flag (skull and crossbones) appears on a TV monitor in 'There's More Than One of Everything', a reference to the Shapeshifter ability to remodel his skull and bones in 'A New Day in the Old Town' (which was filmed directly after this episode).
The car crash in 'A New Day in the Old Town' happens in front of a business called "Gruno & Dunder", an anagram for "underground", foreshadowing the killer's location in 'Night of Desirable Objects'.
FRINGE DIVISION CASE FILE #201-91709
FRINGE EVENT: Shapeshifters
CLASSIFIED CASE CONNECTION(S): N/A
AGENTS ASSIGNED: Dunham, Francis, Jessup
SUPERVISING AGENT: Broyles
FILE ARCHIVED BY: Thomas Ticknor
LOCATION: Boston, MA; NYC
VICTIM(S): Agent Dunham, George Reed, Lloyd Parr, nurse [redacted], Agent Francis (deceased)
CASE REPORT SUMMARY:Official outcome: A random traffic accident involving a federal agent. No extenuating circumstances.
SENATOR: "Unsubstantiated claims of invasion. Reports of technology run amok. The old 'X' designation and your Fringe investigations have been indulgences in the federal budget for over half a century."
PETER: "Na einai kalytero anthropo apo ton patera tou. You said that to me just after you woke up. Do you remember it?"
OLIVIA: "No. Latin?"
PETER: "Mm-mm. Greek. My mother used to say that to me every night before I went to bed."
OLIVIA: "There really isn't a point where things just can't get weirder, is there? What does it mean?"
PETER: "It means 'be a better man than your father'. Walter was already gone. It was like a code between my mother and me. It meant keep your people close. Take care of the people you care about."