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According to When Skeptics Ask (Normal L. Geisler and Ronald M. Brooks, 1990 Baker Books):
The following books were in question at one point or another:
This is somewhat of a side note, but it is worth noting that the thought that some of the books now considered canon were ever disputed might cause some confusion over whether the right books are in Scripture. That is a common question both from the faithful and from skeptics.
My intention here is not to raise the question again. In order to head those questions and comments off, I'll just point out that it's been answered time and time again, as it is here: http://www.worldviewweekend.com/worldview-times/article.php?articleid=1701
Excerpt:
The question which invariably arises when speaking of the Scriptures is, "How does one know which books in today's Bible are the right ones?" It is important to note at this point that a group of men did not just arbitrarily select a group of books to be used in compiling the Bible. They only officially "recognized" which books had always been upheld as being scriptural.
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some details removed. Check the link if you care to see what's missing. Conclusion from the article below:
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A crisis in the fourth century caused the Church to give a formal statement on which books were canonical. In A.D. 397, a Church Council was held in Carthage which endorsed the exact 27 books of the New Testament we now regard as canonical. These 27 books were all apostolic in origin, authoritative in spiritual content, and accepted universally among the orthodox churches. These tests were used at the council to eliminate the spurious gospels and epistles written by heretical groups. This process of canonization has ensured that today's Bible contains only the books which were attested as being inspired by God.
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It appears that certain of the four gospels now considered canonical were once disputed, but Irenaeus insisted that there be four gospels, just as there are four corners of the earth.
Bishop Eusebius of Caesaria, a leading church historian and contemporary of Constantine in the fourth century, wrote the Storia Ecclesiastica, in which he provided the first complete surviving list of what the Christian Bible should contain. He wrote:
It will be well, at this point, to classify the New Testament writings. We must, of course, put first the holy quartet of the Gospels, followed by the Acts of the Apostles. The next place in the list goes to Paul’s Epistles, and after them we must recognise the Epistle called 1 John, likewise 1 Peter. To these may be added, if thought proper, the Revelation of John …. These are classed as Recognised Books. Those that are disputed, yet familiar to most, include the Epistles known as James, Jude, and 2 Peter, and those called 2 and 3 John, either the work of the evangelist or of someone else with the same name.
Eusebius said of Revelation:
As for the Revelation of John, if this seems the right place for it: as I said before, some reject it, some include it among the Recognised Books and so it has remained, but not without argument!
At the time of the Reformation, the canon of the Bible was called into question. Martin Luther condemned the Epistle of James as worthless, and similarly denigrated Jude, Hebrews and Revelation.
Wikipedia lists the seven New Testament books regarded by the Catholic Church as deuterocanonical because they were not universally accepted by the early Church: