Walter's research on LSD-induced hallucinations that can grant the subject clairvoyance is similar to the plot of the book (and later film) Altered States. The film version starred Blair Brown, who plays Nina Sharp.
Among William Bell's books in the episode "Concentrate and Ask Again" is a copy of a book by Dr. Spock. Another Leonard Nimoy reference.
Peter and Olivia meet with a conspiracy theorist who believes himself to be Spock from Star Trek. You should already know who played Spock. More of a Director Allusion, but the story that he tells is somewhat similar to the plot line of Star Trek. However, this was probably intentional as the episode aired in the opening week of the film, and therefore was used to promote it in the process.
The Season 4 finale featured another character played by Rebecca Mader who near death starting talking like a child. Albeit this time Mader's character's mind reverted to a child's after death, not prior to it.
A common fan nickname for alternate universe Walter was "Walternate." Guess what Walter calls him as of episode "Peter."
Altivia, Bolivia, Fauxlivia, or, to some especially uncharitable Peter/Olivia shippers, Holivia. It's worth noting that the fans are fiercely divided on which Fan Nickname to use. The series has decided on 'Bolivia'. Walter has decided on Fauxlivia, however.
And now there's Belivia. Really.
Charlnate (or Scarlie) and Lincolnate - though who the latter refers to is a source of debate among the fandom, since Lincoln is a much more prominent character in the alt universe. Some people have taking to referring to the Lincoln on "our" side as 'Kennedy', since Walter called him that once.
The Polivia shippers call themselves "benchwarmers."
September was renamed Sasstember after he actually makes a joke in 5x11.
Friday Night Death Slot: Was moved here midway through its third season. It's been renewed for season 4, meaning Fringe has actually survived the Friday Night Death Slot, making this only the third Friday/9PM show (after Millenium and Dollhouse) to get renewed since X-Files left.
Although it was likely a coincidence (the name comes from a line of dialogue from the episode), it is amusing that the first episode aired after its move to Friday was "The Firefly," sharing the name of Firefly, another science-fiction show that aired on FOX that was canceled after a move to a Friday timeslot.
Network to the Rescue: Season 4 saw a mild drop in critical acclaim and a large drop in viewers, essentially spelling the end of the show, ESPECIALLY since it was on Fox...right? Wrong! Fox renewed it for a 13 episode fifth and final season instead to let them finish up their story, and bring the episode number up to 100 so that it could be syndicated.