One of Evangelion's most fascinating sides are the various underpinnings to religious and metaphysical theories. The following section points out some of these, but be warned as it includes some spoilers. Most of the information here has been taken from A.D.V films' Evangelion Spotlight.
There are a number of facts about NERV itself that pinpoint the religious influence. The main computer at NERV for example is divided into 3 subsystems which bear the biblical names of Melchior, Balthazar and Casper, collectively known as the three Magi. The codename of the underground base is Central Dogma and the NERV logo reads "Gods In His Heaven. All's Right With The World", which actually is a quote from Browning.

Furthermore the Systema Sephiroticum, drawn by the German priest Athanasius Kircher in 1653, appears on the ceiling of Gendou's office. Kabbalah has his role too, as both the mystical Tree of Life and a Jacob's Ladder being displayed during the opening theme. The Angel Lilith is bound to a crucifix in the Central Dogma pierced by the Longinus Spear (similar to the "Spear of Destiny", which pierced the side of Jesus during the crucifixion)

Back in medieval days the Judeo-Christians took it upon themselves to name and categorize all the angels and demons of the afterlife. The ones of particular interest are the barons of hell.

One baron was said to have a featureless face except for one large eye. (EVA-00)
The baron of darkness was described as having a large singular horn and numerous great gnashing teeth.(EVA-01)
Another baron was described as blood red and a face with four eyes and two mouths.(EVA-02)
The fourth baron was said to be black as pitch and had unnaturally long arms. (EVA-03)

Anno seems to have used the book of Genesis, the "Zohar' and the "Alphabet" to construct the series.
The kabalistic relations are weak but obvious (Shinji - Malkut; Asuka - Hod; Rei - Netzach; Gendou - Gevurah; Misato - Chesed; etc... )

As the second impact happens, a great flood similar to Noah's destroys most of earth' population. Even the cataclysmic explosions that occur during the first combat with an Angel are definetly cross-shaped.

Although the Angels are at first considered to be just invading alien attackers, by and by it becomes obvious that they are trying to steer mankind's destiny. Instead of attacking with joined forces to destroy the humans, each of their deaths result in a step of evolution in the souls of the young children. "Angel" or "Apostel", which would be a more suitable term for "Shitou" seems to be an intended name for the creatures who are obviously working a divine plan to lead earth into a new era of existance.

NERV is not only developing ways to stop the Angels, but on the other hand work on a Human Completion Project to change mankind from a incomplete herd to a complete life-form. This crusade involves extracting DNA of embryotic remains of ADAM, a being found in Antarctica just before the Second Impact happened. Wether ADAM was an Angel or the first human being cannot be determined. However this project is exuse enough for Gendou to use even his own son Shinji as a tool just to reach this goal.

One of the theories making this project plausible is NERV's explanation of living beings, which are seen as vessels each carrying a separate intelligence that can be transferred from one being to another. Evidence for this theory is the existance of Rei, whose clones carry conflicting sets of memories, but also the Evangelions themselves, who act like living beings despite their robot-like appearance. At the same time Evangelions may just be an attachment to human shells, which hold back the evolution of mankind to the next level. The Angels could be seen as beings trying to help man overcome the cling to physical existance, something that prevents us from becoming even closer to God.

Even though the creators of Evangelion have remained quiet on mystical and religious underpinnings, the mythological influence is more than obvious. If one tried to translate the original title "ShinSeiki Evangelion" one would end with "The Gospel of the New Century", leaving us in strange speculations awaiting a new millenium.