There are a lot of shoutouts to famous scientists and science fiction authors.
In one episode Charlie suggests that Olivia see psychiatrist Dr Katz. Must be some Comedy Central watchers on staff.
A conspiracy theorist in "The Road Not Taken" thinks that the entire Z.F.T. conspiracy is caused by "renegade Romulans from the future here to change the timeline" - which is the exact plot of J.J. Abrams' Star Trek movie. The actor who played the conspiracy theorist is Clint Howard, and he played a similar (read "exactly the same") character in an episode of Star Trek: Deep Space Nine.
At one point a copy of Arthur C. Clarke's novel Childhood's End can be seen on a shelf; it now appears that Fringe shares similar overarching themes.
Leonard Nimoy as William Bell. Think about it.
The pilot of is loaded with references to the movie Altered States in the form of Dr. Walter Bishop's shady history as a Mad Scientist. Both Bishop and the Mad Scientist in the movie both combined powerful drugs with sensory deprivation tanks and are naive cloudcuckoolanders with bad social skills. Even their last names are similar, suggesting that Bishop's character might have been inspired in part by Eddie Jessop of Altered States. Furthermore, Amy Jessop in Season 2 has the same last name as Eddie Jessop. Considering Blair Brown is in the cast, this could count as a marginal case of Actor Allusion. That movie was cited as one of the show's influences.
And finally in the season 2 premiere we have X-Files references! First, one character is shown to be watching The X-Files immediately before he dies. Later, a senator makes an in-show reference to "X-designated cases," implying that both the X Files (as in what Mulder and Scully investigated) and "The X-Files" (as in the TV show) exist in the Fringe verse.
In Episode 1x07, Mitchel Loeb refers to "Agents Coscarelli and Scrimm," who are presumably named for horror director Don Coscarelli and actor Angus Scrimm. Scrimm starred as "The Tall Man" in Coscarelli's Phantasm series.
Astrid Farnsworth might be a Futurama shout out, or it might be a shout out to the real Farnsworth.* Almost certainly the latter...by extension if nothing else, since Futurama's Farnsworth is a Shout-Out to the good Dr. Philo.
In 2x13 ("What Lies Below") the CDC shows Olivia a model for what would happen in the disease were allowed to spread. It shows it spreading over the whole world with infected areas in red and non-infected in black. Eventually the whole map is red...with the sole exception of Madagascar.
Speaking of which, here's a somewhat far-fetched one from "Jacksonville"...This is one Ted Pratchett.◊ Could this be a really twisted double allusion to the "trousers of time" theory? (Warning: the image is fairly disturbing.)