Idea #1: Two Vaults. One of them is populated by evangelical Christian families, and the other is populated by secular atheist/agnostic families. Education and entertainment in the Vaults is tailored to each group. The Christian Vault's entertainment choices are tilted towards Christian movies, music, literature and holodisks, while the school curriculum includes intelligent design, abstinence-only sex education, Bible study, lessons on America's Christian heritage, and mandatory prayer at the start of class. The secular Vault's entertainment options, meanwhile, are likewise tilted towards anti-religious and "subversive" ones in much the same manner, and education focuses heavily on science and mathematics, with other classes heavily secularized (the irreligious deism of many of the Founding Fathers, for example, is covered in history, and there is a comparative religion course).
Now comes the fun part. The two Vaults are located within ten miles of one another, they know of each other's existence, and they have contact with one another in the form of telephones, video and a BBS/Usenet-style system. In addition, the respective Overseers are to be elected democratically every year. The experiment will test how ideological unity and conformity, as well as fear of an "other" culture, can lead to extremism. After 40 years, the Vaults are opened up simultaneously, allowing the residents of each, who have been in (indirect) contact with one another for decades, to finally meet each other.
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Idea #2: What I'd like to call the "Big Brother Vault". The residents of this Vault are selected like contestants on a reality show -- in addition to the skills needed to run a Vault, the residents are selected for the traits that will create the most dramatic tension (hey, let's throw in a Black Power guy with a Klansman!), as well as for their more photogenic qualities (i.e. more attractive people). Hidden cameras and microphones broadcast the goings-on in this Vault live to all of the other Vaults (including the two mentioned above) on one of the Vault system's internal TV channels. The only people in the Vault who knows of its true intentions are the Overseer and the backstage staff running the show, who all live in a nearby Vault of their own that is connected to the main Vault but kept secret from its residents. Like the residents, the Overseer will also be selected for photogenity -- he or she is, after all, doing double duty as a TV presenter for all the other Vaults.
There are two changes to the "standard" Vault formula for the people living within. First, every week, a resident must enter the Diary Room for three minutes to record their "private" thoughts which, in theory, will only be seen by the Overseer (in reality, they are broadcasted to the other Vaults). Secondly, every month comes eviction night, when the residents of the other Vaults are able to vote via phone who they want kicked out of the Big Brother Vault. The residents, to keep them from finding out what's really happening, are told that the eviction process is controlled entirely by the Overseer (who is exempt from the eviction process, as are all residents under 16) in order to keep them in line and weed out troublemakers. Evicted residents are taken into the backstage Vault, where they are interviewed by the Overseer and then integrated into that Vault's community. The backstage Vault will have only half the standard Vault population at first, in order to accommodate the influx of evicted Big Brother Vault residents.
This Vault is designed not for any scientific purpose, but rather, like the holodisks and books supplied to the residents, it is meant to serve as "bread and circuses" to keep them compliant.