When Arctor sits on the stage waiting to give his speech to the Brown Bear Lodge, one of the images his scramble suit displays is Philip K. Dick. This is a clever reference to the novel, in which the scramble suit is said to show the likeness of its creator once in every several million permutations.
Robert Downey Jr. wrote most of his lines down on post-it notes and scattered them around the set so he could read off them while filming a scene. The rotoscoping team simply animated over the notes to remove them from the film during post-production.
In 1976, an interview with Philip K. Dick was recorded for California radio station KPFK-FM in which he read a passage from A Scanner Darkly, the scene in which Charles Freck unsuccessfully attempts suicide. Director Richard Linklater remarked in an interview that he wanted to use this recording in the film during this scene, but that it was in such poor condition as to be deemed unusable. The passage, nearly word for word from Dick's novel, is read instead during the scene by Leif Anders.
The title is an appropriation of 1 Corinthians 13:12, which reads, in part: "For now we see through a glass darkly; but then, face to face: now I know in part; but then I shall know even as I am known."
This is the highest-grossing digitally rotoscoped animated feature, grossing $7,659,918. However, being also the most-expensive rotoscoped feature ever made, that figure is lower than the film's cost of $8.7 million.
A theme of bears can be noticed in the film - the meeting at the start is of the Brown Bear Lodge; a California state flag (with a bear on it) is seen in Arctor's house; Arctor's name appears to be derived from 'Ursus arctos', the scientific name for the Brown Bear and from the star, Arcturus (located in the Bootes constellation which is also known as the 'bear keeper/ herder').
(at around 1h 5 mins) When Arctor is going through the second phase of testing with the medical deputies, the laptop-like machine on which he is being tested is branded as V K mk1. V K stands for Voight Kampff, the test used in "Do Androids Dream of Electric Sheep" (a.k.a. "Blade Runner") by Philip K. Dick, where the test is used to measure the response time and the involuntary reaction of the pupil of the eye, in short, an emotional reaction to determine whether they are humans or androids.
In Arctor's kitchen there is a drawing of a head in a box next to the phrase "Time to thaw Walt out!". This is a reference to the urban legend that animator Walt Disney had himself cryogenically frozen.
(at around 1h 5 mins) When Arctor and Connie are about to have sex, there is a brief view of the clock/radio next to the bed. The clock shows the time as 4:20, a classic drug reference, fitting in with the theme of the film.
Charlie Kaufman wrote a screenplay adaptation of the novel with Australian director Emma-Kate Croghan. He couldn't produce a usable script and when his profile swelled with the success of Being John Malkovich (1999), he lost interest in the film. When the project changed hands, Kaufman's script was no longer involved.
"Clerodendron Ugandens", the source of the organic component of Substance D is apparently based on a real species of flower - "Clerodendrum ugandense", the blue glorybower. However, it has been reclassified and is now known under the correct name "Rotheca myricoides". Like the movie asserts, the plant is highly poisonous to humans and livestock.
(at around 30 mins) In one scene, Barris unsuccessfully attempts to create a pistol silencer, disturbing the people around him with loud gunshots while testing it. Sherlock Holmes (2009) also features a character played by Robert Downey Jr. doing this.
The Red Pills known as Substance Death, a drug that alters a user's reality, bear a striking resemblance to the Red Pills given to the character Douglas Quaid in the film Total Recall (1990) that, in this instance, are used to bring Quaid out of the Rekall Memory Implant-induced reality.
Both the lodge number and Arctor's house address are "709". This is a reference to the famed Austin satirical rock band "Uranium Savages", who use 709 as a "secret" number. All Uranium Savages fans are familiar with this and the director likely inserted the number as homage to the band.