You're likely thinking of so-called "Lost Books of the Bible". They don't exist. This is a common idea based upon a lack of knowledge about how the Biblical Canon came to be.
For one thing, none of the so-called "Lost Books" are actually lost, many of them were well attested to in antiquity and we have a bunch of them today, many can be found online, translated into English if one wanted to look for them.
The Bible did not suddenly poof into existence, it is the product of hundreds, and hundreds of years of Christian tradition.
The earliest Christians would have almost certainly understood "the Scriptures" to refer to the Septuagint, a translation of the Jewish scriptures into Greek done in Alexandria roughly three hundred years before Christ. As Christianity was predominantly spreading to Greek-speaking communities of Jews, God-Fearers (Gentiles who revered the God of Israel but had not yet formally converted to Judaism), and Pagans it was only natural that the early Christians would have made use of those holy writings that were readily available.
This was also a time when Judaism was far from monolithic and did not have a strict canon of scripture to speak of (what eventually became the Tanakh).
Like Jews before them part of Christian worship and liturgy involved the reading of Scripture, and as the Christian community began to grow other books began to be circulated and read in the churches as well, some of the earliest were most likely Paul's epistles which were letters addressed to various Christian communities and likely began to be circulated and read. When, exactly, Paul's epistles started to be treated and venerated in the same way as the Septuagint is uncertain, but definitely no later than the late 1st or early 2nd century.
During the course of the 2nd century there were a number of books being read in Christian communities all over the place, some were received almost universally while others were subject to debate (some of these books are in our current New Testament, such as James, Jude, 2 Peter, 2 and 3 John, and the Revelation of John; some of these books are not in our current New Testament such as the Epistle of Clement, the Epistle of Barnabas, the Didache, the Shepherd of Hermas and the Revelation of Peter).
However, the debated books were a very select number. Claims of "hundreds of gospels" for example is patently false. There were lots of texts with the term "gospel" attached to them, but other than the Four (Matthew, Mark, Luke and John) none were ever anything other than special, private texts for specific sects and communities (the Ebionite sect, for example, had their own gospel known as the "Gospel of the Hebrews").
Over the early centuries these conversations continued, in the third and fourth centuries various religious leaders and a few regional councils would go out of their way to define what was canonical, what was not canonical, and what was "iffy" and not everyone was in complete agreement. For example, in the fourth century St. Athanasius offers a list of books he regards as canonical and lists what are to be regarded as apocryphal, in it he lists Esther as NON-canonical.
Our earliest biblical codices (that is, near-complete Bibles) date from the fourth and fifth centuries (we have papyri manuscripts much older than this of course) and show some diversity. An example is the fourth century Codex Sinaiticus which is a remarkably complete biblical codex and contains the books we are usually familiar with but also includes the Epistle of Barnabas and the Shepherd of Hermas--two of the disputed books.
Some books were more widely accepted in some areas than in others. In the West the Revelation of St. John (Book of the Revelation) was received quite early, Western Church Fathers such as Justin Martyr and Irenaeus attest to its importance and authenticity. In the East it's a very different matter, and it wasn't until the time of St. John of Damascus (7th-8th century) that the Revelation finally became fully accepted as canonical in the Christian East. In fact this may be seen reflected in the fact that the Eastern Orthodox Church, in its lectionary, has readings from every book of the Bible except the Revelation.
The New Testament, more or less, came into its final form in the fourth and fifth centuries, though as noted above it continued to evolve to some degree here and there.
The Old Testament, however, has its own unique history.
As noted, the earliest Christians almost certainly used the Septuagint. As the Christian and Jewish communities separated during the last half of the first century, this was likely one of the major diverging points. Christians continued to use the Septuagint, while the Jewish community increasingly began to define its Scriptures based on what, arguably, had originally been written in Hebrew (and certain books of the Septuagint more than likely were originally composed in Greek).
Some Christians came to debate some of these books, though generally the Septuagint remained as-is. In the Western Church, during the 5th century, it was seen that a new translation of the Bible was needed to be made into Latin, specifically in the Vulgar (Common) Latin of the people. So the Bishop of Rome commissioned Jerome to the task, Jerome (who was living in Bethlehem at the time) questioned the legitimacy of those books found in the Septuagint, but not in the Jewish Tanakh (such as 1 and 2 Maccabees, Tobit, Judith, Sirach, etc). Nevertheless Jerome translated all of it, and this became known as the Vulgate (Latin: Vulgata, a Bible in the Vulgar/Common tongue).
During the Protestant Reformation, while questioning a lot of other things, Reformers such as Martin Luther questioned the canonicity of these books (he also questioned the canonicity of some of the New Testament books, but ultimately left them alone). The Deuterocanonicals (as they are technically called) he moved in his German translation to an appendix between the Old and New Testaments under the heading of "Apocrypha". He, along with many of the other early Protestants, saw that these books were good and should be read by Christians but understood to be inferior than the rest of Scripture. This was common in Protestant Bibles for a while, the original publishing of the Authorized Version (KJV) in 1611 contained the Apocrypha. These were only fully removed from Protestant Bibles by later Protestants.
In response to the Protestant Reformation the Roman Catholic Church had its own Counter-Reformation, and part of that was the Council of Trent. This was the first time a general council had been convened (though its only recognized by the Roman Catholic Church as ecumenical) which defined the Biblical Canon. At Trent most of the Deuterocanonicals were retained, but a few were left out.
For this reason, while Protestant, Catholic and Orthodox New Testaments are identical, the Old Testaments of each differ from each other. The Orthodox Old Testament is, basically, just the Septuagint. The Catholic Old Testament is the Old Testament defined by the Council of Trent. The Protestant Old Testament is what was generally agreed upon by the Protestant Reformers.
But rest assured that no conspiracy happened to take "bad stories" out of the Bible, they were never there to begin with and were never up for consideration for inclusion into the Biblical Canon. Gnostic Gospels such as that of Judas or Philip were never no more likely to be canonical then Plato's Timaeus or Homer's Odyssey.
-CryptoLutheran
