This is a huge question and therefore cannot be answered in a few hundred words. In light of this, let me give you two important developments that burgeoned from the Early Middle Ages until 1600.
One of the most significant developments in the intellectual life of Europe was the Renaissance. The reburgeoning of classical learning - partially from people who came over from Constantinople - created an atmosphere that sought to go back to the classical world and its glories and even to excel it. For example, there was a buzz word, "Ad Fontes," which can be translated into "back to the sources." This ethos created a confident society that sought to overcome the heights of the classical world.
Second, the Protestant Reformation was another huge development. This movement challenged the power of the Catholic church and it was in many ways an intellectual religious movement that took the fruit of humanism and applied it to biblical texts. For example, John Calvin's first book was not a religious tract, but a work on the Roman philosopher, Seneca.
In a word, both the Renaissance and Protestant Reformation were great intellectual movements that shaped Europe and even the modern word.