What Is Canon?
The Tiers of Canonicity
One of the difficulties in analyzing Neon Genesis Evangelion is the large number of secondary sources, some of which seem to be contradictory. Just how does one determine what is and is not canon? A very handy rule of thumb was invented for this purpose by Shin-seiki, a frequent poster at the Anime Nation and Eva Monkey forums. This tool is know as Shin-seiki's Tiers of Canonicity and it is what we use here:
1. The anime itself and its scripts and storyboards. The Director's Cuts are the final or official version and take precedence over the On Air version in the event of any theoretical contradiction.
2. Statements made by the show's creators, principly Hideaki Anno.
3. Official suplemental sources such as theatrical programmes, Newtype Filmbooks, and Cardass Cards.
4. The Manga, which is actually its own continuity. At best it can be used to support the anime when they are in explicit agreement; it should never be used to contradict the anime.
5. Statements made by those responsible for adapting Evangelion for release outside of Japan. In the English speaking speaking world this would be representatives of ADV or Manga Entertainment.
Lower tiers are canon only if they do not contradict the evidence presented in higher tiers. Info from lower tiers should also be treated with somewhat more skepticism than higher tiers.
The following are some examples of each tier.
Tier 1: The Anime Itself and its Scripts and Storyboards:
The primary Canon is the evidence presented in the series. For example, when Misato reveals to Shinji in Ep. 19 that all of his classmates are Eva pilot candidates, that is official. It could not be contradicted by any lower tiered source. You can then combine it with evidence from elsewhere in the show such as Toji's implication in Episode 3 that his mother is dead, and the revelations that the souls of Unit-01 and Unit-02 are the pilots' mothers, and conclude that Unit-03's soul is that of Toji's mother.
The scripts and story boards have yielded some important gems of information. For instance, the script for Ep. 22 already describes the Lady Doctor as Langley's mistress. Another example would be that the script for The End of Evangelion explicitly describes the "Mother" from the sandbox scene as Misato.
Everything added to the director's cuts is first tier canon and was put there to set up something that happens in EOE. Shin-seiki has promised to write an essay that will go over this scene by scene.
Tier 2: Statements made by the show's creators, principally Anno.
The most famous example of this is Anno's statement that Kaji was not shot by any of the main characters, but by a nameless assassin sent by either Nerv's or Seele's security devisions. Anno rarely comments on NGE, so when he does you know that he feels that it's an important issue. In this case he was so shocked that many people believed that the assassin was Misato that he issued an explicit denial. As there is no credible evidence in the only higher tier, the series itself, that Misato is the assassin, Anno's statement is canon.
Note: The Confidential Information is said to have come straight from Anno. Provided that this is true, it should be considered Tier 2, not Tier 3.