Who decided what goes in the Bible? Was there any political agenda behind what was put in? If so, how do we know what to trust and what to be skeptical of? Also, what else are we missing that could be important?

The Old Testament was essentially completed by 400 BC, ending the Word of God that had begun with Moses in about 1500 BC. As these Scriptures came together, so did ways of evaluating their truthfulness as Scripture: (1) Was it written by a prophet, that is, a spokesman from God, (2) was that person confirmed as a prophet by God by miracles or other means, (3) was the message consistent with other Scriptures, (4) did it reveal the life-changing power of God, and (5) was it accepted as Scripture by making people respond to its truths. It was the Bible to which Jesus referred as He taught during His ministry. A Jewish council (a meeting of scribes and elders) confirmed the content of the 39 books of the Old Testament at a council at Jamnia (90-118 AD). To maintain the integrity of these scriptures, a group of Jewish scholars called “Masoretes” were entrusted with the task of making copies of these Hebrew writings. They were active during the years 500-900 AD. They developed an incredibly detailed system of counting the number of words in each book of the Bible and in each line of each page of each book to make sure they had copied it accurately. Any scroll found to have a mistake was taken away and buried according to Jewish law. The trustworthiness of this process came to light in 1947 with the discovery of the “Dead Sea Scrolls.” One of the documents discovered was the book of Isaiah—virtually complete. Dated from 150 BC, it matched up virtually word for word with the previous oldest documents that we possessed at the time—from 980 AD!
As for the New Testament, those books were written over an approximately 60-year span of time, from the 40s to about 100 AD. The 27 books that make up the New Testament were evaluated in this way: (1) Did the book have apostolic authorship—either a direct apostle of Jesus or one of their followers, (2) Was the book authoritative, (3) Was the book consistent with the rest of recognized Scripture, and (4) Was the book accepted as Scripture by the church. By the end of the fourth century (397 AD at a church council in Carthage), the 27 books of the New Testament were likewise recognized as Scripture—coming from a unanimity of viewpoint from the churches then in existence that had long ago recognized the true Scriptures while rejecting others. There was no agenda except the agenda of the leading of the Holy Spirit; as New Testament scholar F.F. Bruce said, “The historic Christian belief is that the Holy Spirit, who controlled the writing of the individual books, also controlled their selection and collection.” This only makes sense, as one of the ministries of the Holy Spirit according to Christ was that when he, the Spirit of truth, comes, he will guide you into all the truth. He will not speak on his own; he will speak only what he hears, and he will tell you what is yet to come—Jesus Christ, John 16:13.
The liberal Christian viewpoint, perhaps best embodied by the group the Jesus Seminar, has tried to make a case for other “gospels,” written in the second and later centuries, often coming with the name of someone well-known in Jesus’ time but that have nothing to do with their real authorship. As such, they fail one of the tests of genuine New Testament authorship—direct apostolic connection to the Savior. Maybe one of the best examples of this is the Gospel of Thomas. Liberal Christianity asks, Why can’t this be as recognized a gospel as Matthew or Mark or the others? Decide for yourself: Here’s a quote from this book, attributed to Jesus: “Lucky is the lion that the human will eat, so that the lion becomes human. And foul is the human that the lion will eat, and the lion still will become human.” And, if you are a woman, you’ll love this quote from Jesus; at one point, Peter is complaining, saying, “Make Mary (Magdalene) leave us, for females don’t deserve life.” And Jesus responds, “Look, I will guide her to make her male, so that she too may become a living spirit resembling you males. For every female who makes herself male will enter the domain of Heaven.” Really? Your response is how the church responded, both to the gospel attributed to Thomas and to many others (maybe as many as 18) that were in existence in the early centuries of the church, as well as the apocryphal books that the Catholic church much later added to their canon to validate some of the doctrines that separated them from Protestants.