The Final Five escaped the nuclear holocaust on Earth several thousand years prior to the events of the series. They developed resurrection technology, and traveled (without faster-than-light drives, hence the amount of time it took) to the Twelve Colonies to convince the humans not to repeat their mistake and develop artificial life again. They were too late, as the humans were already at war with the Centurions, who had begun to create humanoid life (the Hybrids).
The Final Five gave the Centurions resurrection technology and developed eight humanoid models, the seven known models and "Number Seven," or "Daniel." The Number Seven line was apparently wiped out entirely by the Cavils (Number Ones).
So, apparently (as of this episode), there were actually 13 Cylon models, though only 12 now exist.
This episode opened with a completely new introductory sequence with the following text:
This has all happened before
and it will happen again
The Cylons were created by Man
Then they vanished
Forty years later they came back
50,298 human survivors
Hunted by the Cylons
Eleven models are known
One was sacrificed
Laura Roslin: (to Lee) My only concern about you is that you're so hell-bent on doing the right thing that you sometimes don't do the smart thing.
Tigh: Yeah, you point a finger back far enough and some germ gets blamed for splitting in two.
Ellen: Hello John.
Cavil: I don't care for that name. I think you know that.
Ellen: I named you after my father.
Cavil: And you made me in his image. Thanks a million for that.
John Hodgman, well known as the personification of PC in the recent Apple Macintosh commercials, appears in a guest role as Dr. Gerard.
James Callis is listed in the opening credits but does not appear in this episode.
As of the main title sequence, there are 39,556 survivors remaining in the Colonial fleet, 47 fewer than at the beginning of the previous episode.
When John was talking to Ellen in the resurrection chamber, he said that her ancestors did not crawl out of the swamp. This is a glib reference to the scientific theory of evolution and its explanation of the origins of humanity.
When Cavil leaves Ellen and Boomer alone to talk, Ellen offers Boomer an apple. This is a likely reference to the Book of Genesis in The Bible and the "fruit" from the tree of knowledge of good and evil. Satan convinced Eve to eat the fruit of the tree. Eve in turn convinced Adam to eat the fruit.
Cavil could be taking on the role of Satan, with Ellen as Eve. It should be pointed out that the Biblical text never mentions an apple but most people think of the fruit of the tree of knowledge as an apple.
Furthermore, the consumption of the fruit is often thought of as a metaphor for sexual relations, that Eve had intercourse with Satan. Likewise, Ellen had engaged in sexual intercourse with Cavil in a previous episode, although the parallels get confused in terms of the creator-creation relationship between Cavil and Ellen.
Ellen was trying to get Boomer to realize the difference between her philosophy and that of Cavil, and then to choose a side. That could be a more literal take on the idea of the apple representing knowledge of "good" and "evil".
Ellen mentions "the swirl" to Boomer, a reference to Ellen's sexual relationship with one of the Cavils on New Caprica in the Season 3 episode "Precipice". In the podcast for "Precipice", Ronald Moore confirmed that the use of the term "the swirl" in that episode was itself an allusion to the Seinfeld episode "The Fusilli Jerry". Ronald Moore is a fan of the Seinfeld series.
The episode title may refer to the traditional English-language translation of the title of Jean-Paul Sartre's 1944 existentialist play, Huis Clos. The play includes perhaps the most famous line from the French philosopher, "L'enfer, c'est les autres" or "Hell is other people."