Fringe Connections

Walternate has three solid-color panels on the wall of his office in "Bloodline": blue, red, and yellow. These symbolize the two universes (blue and red) and the rewritten timeline without Peter (yellow) starting from "Neither Here Nor There".

Olivia pulled up a list of the frozen heads found in S02E04 'Momentum Deferred' and they were all marked with "2E204", a reference to the episode in which they were stolen.

A seahorse can be seen outside the entrance to the daycare center.

A butterfly shadow box like those seen in "The Dreamscape" was seen in Walter's storage vault in "The Bullet that Saved the World".

There is a Massive Dynamic logo on Flight 627's engine.

A leaf can be seen on the bio-scan monitor at the Liberty Island security checkpoint.

The ship at the end of "Nothing as it Seems" showed the creatures from "Snakehead".

When Walter explains that his red/blue lensed glasses were created by his friend from Washington, Doctor Jacoby, he's referencing the television show 'Twin Peaks' which also had an eccentric man of science, Doctor Jacoby, who wore red/blue lensed glasses very similar to Walter's.

A hand can be seen outside the entrance to the daycare center.

In "Liberty" the Fringe team used the universe window from "Peter" to help them rescue Michael.

The Fringe team is part of a full-fledged branch of the Department of Defense in the Redverse.

A butterfly can be seen painted on the side of a white trash can.

Despite Walternate's efforts to mold Olivia's mind into Fauxlivia's, Olivia kept seeing Peter and Walter in "Amber 31422". Similarly, in "Alone in the World" Peter didn't exist in the rewritten timeline yet Olivia kept having visions of him.

Bell stole Walter's David Bowie album 'The Man Who Sold the World', which describes what Bell did multiple times for his own benefit.

The frog glyph can be seen on a door in the pocket universe.

The nanites in "Brave New World (Part 1)" have an "X" on them that matches the "X" on the shirt worn by the man Peter freed from Olivia's mind in "Lysergic Acid Diethylamide", suggesting that "Mr. X" from Olivia's mind may have been William Bell (who was ultimately behind the nanites).

Windmark visited his boss, The Commander, in 2609.

The butterfly glyph can be seen on the wall in the diner where Olivia and Lincoln meet.

In "Os" Peter revealed to Olivia that he was working on the Shapeshifter devices that he collected in "Reciprocity" by killing Shapeshifters.

Walter's pose as he listens to the Mozart Requiem is a reference to the iconic Maxell tape advertisement from the '80s.

A butterfly can be seen on a lampshade near the front of Olivia's apartment.

Windmark probed Walter's mind so forcefully in "Transilience Thought Unifier Model-11" that it caused blood vessels in Walter's eye to pop. In "Liberty" Michael resisted Windmark's mind probe, and possibly probed Windmark's mind back, causing blood vessels to pop in Windmark's eye.

Donald helped Walter set up the pocket universe hiding spot.

The leaf glyph is on the electronic keypad at Massive Dynamic.