I’m re-watching my Fringe Blu-rays and remembering all of the times the show has referenced Twin Peaks.

• An episode in the second season is called “Northwest Passage” and follows Peter to Washington state, where he helps solve the murder of a young woman (wrapped in plastic) in a sleepy coastal town. “Northwest Passage” was the original working title of Twin Peaks, a show set in Washington state and centered on the murder of a young woman, Laura Palmer, discovered wrapped in plastic.
• In the season three episode “The Firefly,” Walter dons a pair of red and blue 3D glasses. Astrid tells Walter that the glasses look good and Walter responds, “These were created by an old friend of mine, Dr. Jacoby from Washington state.” Dr. Jacoby was the name of Laura Palmer’s therapist on Twin Peaks, and he did indeed don those red and blue frames. 
• Walter’s mistress in the season three episode “Immortality” is played by Joan Chen, who played Josie Packard on Twin Peaks. 
• In the same episode, a character named Anton Silva orders a slice of pie and a cup of coffee at a restaurant, not unlike Dale Cooper. The name Silva is also a reference - the actor who played the mysterious B.O.B. on Twin Peaks was named Frank Silva.