Pilot

FBI Agent Olivia Dunham is called in as an inter-agency liaison when all passengers and crew on international flight 627 from Hamburg, Germany to the USA are killed by an airborne compound which causes the skin to rapidly degenerate and dissolve.

Olivia and her fellow agent and lover John Scott encounter their suspect conducting research in a series of storage garages. Olivia seeks the help of institutionalized scientist Walter Bishop, a former chemist who conducted research into "fringe science" - experimenting with elements of the paranormal. In order to get Walter to co-operate, and secure his release from the psychiatric hospital, Olivia must convince Walter's son Peter Bishop to reunite with his father and aid their search for a cure. Along the way, Olivia discovers that the flight 627 incident is just one in a series of unexplained incidents being referred to as The Pattern and that it may be more than just a simple act of biological terrorism.

Synopsis provided by the Fandom Wiki, Fringepedia, and Wikipedia.

• Timestamp: 08:01
  There is a Massive Dynamic logo on Flight 627's engine.
• 
  Charlie said "Logan is one of the first airports with the PEARL autopilot system." This system was designed by Massive Dynamic.
• Timestamp: 12:25
  There is a Massive Dynamic logo ('MD') on the car found in the storage unit.
• Information about Peter: he's a high school dropout who worked many jobs including being a fireman, cargo pilot, and college chemistry professor. He falsified his degree from MIT, and he speaks Farsi.
• William Bell, the head of Massive Dynamic, shared a lab with Walter long ago.
• The Massive Dynamic billboard says 'MANDALA', possibly a purposely misspelled reference to the Mandela Effect, a phenomenon of false memories often shared by many people. A well-known example of a widespread false memory is many people thinking the Berenstain Bears books from their childhoods were actually spelled Berenstein Bears. The notion of personal and widespread false memories becomes a big theme in Fringe.
• The Kresge building mentioned in this episode is a real building at the Harvard School of Public Health.
• The text on Broyles' whiteboard is from a real Homeland Security document.
• Timestamp: 51:20
  The canoe in Olivia's dreamscape says "Zeno", a possible reference to Zeno's Paradoxes. "Whereas the first two paradoxes divide space, this paradox starts by dividing time." Or it could be a reference to the Massive Dynamic website which says "What's next? Travel time follows a power law, decreasing by a given factor year by year. MD's Zeno-Transit Initiative aims to take that process to the limit, making near-instantaneous travel a reality in your lifetime."
• The canoe has an aleph on it (Phoenician alphabet).
• Timestamp: 51:27
  The tombstone in Olivia's dreamscape says "He's Not Dead."
• The pole outside Massive Dynamic has an ad for glowingmonkeys.com, which has the tagline "I know they're watching, from the dark...".
• The idea for Massive Dynamic was likely inspired by real companies such as Boston Dynamics and/or General Dynamics.

• The pilot episode opens with a plane incident, and Morgan Steig is passenger number 108, both references to Lost. Lost
• The theme song (in this episode only) has a flip-board-like sound in the background (similar to the countdown timer sound in the hatch in Lost).
• Walter worked for a classified U.S. Army experimental program called Kelvin Genetics. Kelvin
• The Massive Dynamic billboard seen here references "Credit Dauphine", a fake financial organization seen in Alias.

Lost

Lost is famous for its number sequence 4-8-15-16-23-42 and the sum of those numbers, 108.

Kelvin

J.J. Abrams projects tend to feature the name Kelvin, his mother's maiden name.