Behind the Folklore -
Are You There, God? It's Me Dean Winchester

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APOCALYPSE
Apocalypse technically refers to a revelation of God's Will (The Bible). Thus, in Revelation, we see a clear pattern of future events: the various periods of the church, shown through the letters to the seven churches; the throne of God in Heaven and His Glory; the judgments that will occur on the earth; the final form of gentile power; God' re-dealing with the nation Israel based upon covenants mentioned in the Old Testament; the second coming proper; the one-thousand year reign of Messiah; the last test of Mankind's sinful nature under ideal conditions by the loosing of Satan, with the judgment of fire coming down from Heaven that follows; the Great White Throne Judgment, and the destruction of the current heavens and the earth, to be recreated as a "New Heaven and New Earth", ushering in the beginning of Eternity.

In Supernatural, Castiel is sent to warn Dean of the opeining of the Seals and the impending Apocalypse. In Apocalyptic religious writings, the introduction of Angels as the bearers of the revelation is a standing feature. At least two angel-classes are mentioned in biblical scripture: the Cherubim and the Seraphim. God may give instructions through the medium of these heavenly messengers, and who act as the seer's guide. God may also personally give a revelation, as is shown in the Book of Revelation through the person of Jesus Christ.

66 SEALS
A Supernatural plot device in this case. Loosely based, I assume, on the 7 seals, which is a concept of Christian eschatology, found in the Book of Revelation in the Christian Bible. It states that when the world reaches its end, seven "seals" will be opened. A book with seven seals is first mentioned in Revelation 5:1. In chapter 6, the first six seals are opened by The Lamb (presumably Jesus), one by one. Then 144,000 are sealed at chapter 7(Revelation 7:4) in legions of 12,000. Chapter 8 begins with the opening of the seventh seal, and a gold censer with a gold altar of incense before God's throne (mercy seat)(Revelation 8:1). The first four of the seven seals are commonly referred to as the four horsemen / four horses of the Apocalypse.
Bible scholars associate the seven seals with the seven Spirits of God, and other Bible 'sevens'. The seals contain symbols commonly interpreted as death, famine, world wars, martyrdom, earthquakes, and the Antichrist. It also states that there will be "seven trumpets" announcing aspects of the "End Times": mankind being judged, seas turning to blood, sores on people's bodies, plagues, infertility, and the introduction of "seven bowls" (in King James Version called "vials"). These bowls are a third each of the sea, humankind, water, animal life, ships, crops, and earth, all engulfed by an infinite abyss.

WITNESSES
While researching into the apocalypse, I came across information on the book of Revelations in the Bible. The Chronology of Revelation details a series of events which take place in the Book of Revelation, detailing (by some accounts) the final judgement of God on the world, in the final Book of the Christian Bible. The events portrayed in Revelation are full of symbolism, imagery, and metaphor, with a wide range of interpretations as to how the events should be perceived.
Revelation 11 introduces two witnesses, who are described as "the two olive trees and the two lampstands that stand before the Lord of the earth". They will prophesy for twelve hundred and sixty days, clothed in sackcloth. The witnesses will be given supernatural powers to defend themselves from attack and to smite the earth with plagues. They will "torment those who dwell on the earth" with these plagues. After they prophesy and testify for 1,260 days, the beast that comes up out of the abyss will make war with them, and overcome them and kill them. Their corpses will lie in the streets of Jerusalem for 3-1/2 days while the world watches and rejoices over their deaths. However, after the 3-1/2 days, they will be resurrected and then ascend into heaven while their enemies look on.

Other signs include The Beast from the Sea and the Beast from the Earth, both of which will have everyone wear his mark on their right hand or forehead. (I assume this is how the marks on the Witnesses came about)


OTHER REFERENCES
Dean: All I know is I was not groped by an angel.
A play on the show titled Touched by an Angel (1994-2003) starring Della Reese and Roma Downey, about angels who live among people, influencing their lives.

Bobby: If you're going to shoot, shoot. Don't talk.
This quote is from the classic western The Good, the Bad and the Ugly (1966) written and directed by Sergio Leone. A gunslinger, a hit man, and an outlaw go after a dead man's gold during the American Civil War. Starring Clint Eastwood, Eli Wallach and Lee Van Cleef. The line is said by Tuco (Wallach) during a similar scene as we see here.

Dean: You know, Michael Landon, not dicks.
Referencing Highway to Heaven (1984-1989), starring Michael Landon as Jonathan Smith, an angel sent to Earth to help people with the aid of human Mark Gordon (Victor French).


Sources: Wikipedia, TV.com