What was religion like in the Middle Ages? Was it dominated by Christianity or was pagan folk magic still a norm? How was Judaism or Islam looked at in feudal Europe? Could you spilt the answers from the begin, middle, and end of the medieval times?

As always, the answer depends on the time and place. Medieval Christendom was a large place with many different opposing perspectives on religion. Trying to make any summary, is as previously stated, a tall order.

The general strand is that people in Christendom were Christians**. Of course, what exactly that Christianity was is subject to many asterisks. I will narrow my answer down quite a bit to areas I know a bit more of. In the modern day, religion is something forward-looking. It is the way a practitioner communicates with their future, their experiences in the afterlife, etc. In the Middle Ages, religion was part of the lived experience of people. Stories abound about nature spirits, river ghosts, demons, monsters, etc, all nominally pagan stuff. In a premodern state the enforcement of religious orthodoxy is impossible.

I will discuss Byzantine Greece here, for I know a little bit about it. I am aware that by this point, Greece itself was on the periphery of the Byzantine world. I'm sure there were some differences to the politico-religious situation in Asia Minor. None of this is by itself indicative of the whole of the Orthodox world.

Be it known that the inhabitants of Castle Maina [Mani] are not from the race of aforesaid Slavs (Melingoi and Ezeritai dwelling on the Taygetus) but from the older Romaioi [‘Romans’, i.e. ‘Christians’], who up to the present time are termed Hellenes [‘Greeks’, i.e. ‘pagans’] by the local inhabitants on account of their being in olden times idolaters and worshippers of idols… [but] who were baptized and became Christians in the reign of the glorious Basil. The place in which they live is waterless and inaccessible, but has olives from which they gain some consolation. - Constantine VII, Emperor of the Romans

The Maniotes were notable for their crypto-paganism, as well as their fierce resistance to central control. Through the rule of Rome, Bulgaria, and the Ottomans, the Maniotes never were firmly integrated into any of the three. In this vein they were rather similar to the Scottish highlanders, Bretons, and the rest of the Balkans in general. While Slavic invasion displaced many pagans, their religious aspects continued to survive in a population that was impossible to educate about actual orthopraxy. This was especially prevalent in mountainous regions, which Greece and the Balkans definitely qualify as. Another notable such group were the Sarakatsani. They lived in the mountainous regions of Rumelia (Northern Greece) as sheep herders. The Sarakatsan clans practiced a brand of Christianity divorced from that of Constantinople. They had no concept of the Holy Spirit, instead believing in a double hybrid God called Ays (or Hagias), that sort of encompassed God the Father and the Son. They believed heavily in folk magic and nature spirits.

Another notable Balkan holdout were the Bogomils. Bogomilism is a form of Gnostic Christianity heavily focused on the duality between good and evil. The Gnostic tradition was born in the Late Antiquity Middle East, amidst persecution both from Rome and Zoroastrian Iran. Gnosticism took on elements from Buddhism, Judaism, Christianity, and Orthodox Zoroastrianism. Bogomilism in the Balkans was an outgrowth from earlier sects in Asia expelled there. In the Balkans it was adopted by some Bulgarians, and was bounced around quite a bit. The Slavonic sources are all unanimous in condemning Bogomilism as Manichaean. It was a prominent religious movement in the Medieval Balkans and was linked to other sects like Waldensians and Cathars.

When I say religion was a lived experience in people's lives, I mean just that. A local herdsman could name all the local spirits who protected his flocks, worship rippling ponds as reflection of God, and when foreign invaders or bandits came, retreat inside the walls of his nearest town and chant the orthodox Akathist, properly.

I have given only a short geographic snapshot but hopefully you understand the diversity of the religious situation. Religious Orthodoxy is largely an invention of the Early Modern and Enlightenment age. With the expansion of the printing press and expansion of the state also came expansion of the Church. Voltaire frequently wrote to Catherine encouraging her to rid her Tatar subjects of their beastly religion; she instead ordered the Quran printed and distributed. Even here, religious syncretism in Europe survived well into the modern age. Throughout the 19th century and into the early 20th century, the mountainous Balkans and Italy maintained "weird" villages. That is part of what allows some specific examples to come down to us; the Sarakatsans would not have written about themselves and we would not know of their practices if not for people like Patrick Leigh Fermor.