The Cathar church was inspired by gnosticism, a group of Christian heresies which went extinct in the IVth century. Like gnostics, cathars believed that humans had a divine soul that would reincarnate until humanity went extinct. For them, souls had no gender (a man could get reincarnated as a woman and vice-versa), therefore men and women were equal. If I'm not mistaken, they also believed that having sex was a good thing, but that having children was a sin because it would force a soul to reincarnate against its will. Cathars were generally opposed to the use of violence, but they would still use it in self-defense, whereas earlier gnostic groups advocated violence as a mean to hasten the destruction of humanity. This was a key point of difference, though the Catholic Church may have exaggerated the similarities between cathars and gnostics as a way to discredit them.
The Druze religion is based on a mix of Islam, Christianity, and hellenic (mostly Platonician) philosophy. They also believe in (a form of) reincarnation, but unlike cathars they do not believe that matter in inherently evil. They think that the goal of life is to attain wisdom, though they apparently have a reputation for not talking about their religion with non-believers. From my research, they apparently have more in common with Sunnism than with Shia Islam (so the game might be misleading on this point), though I might be wrong on this one.
The Manichean religion is represented as a Zoroastrian heresy in-game, but that's not quite what it was. It was a blend of Buddhism, (gnostic) Christianity and Zoroastrianism, created by a self-proclaimed prophet named Mani who lived in the Persian empire. They believed that Good and Evil were in constant struggle (like Zoroastrians), but also that all flesh was evil and that Jesus was never fully human (two typical gnostic ideas), and that the circle of reincarnation could be stopped by self-discipline as taught by Siddhartha Gautama. However, they were insistent that the teachings of Buddha, Jesus and Zoroaster were incomplete and had to be completed by Mani, whom they believed to be the Paraclete or Holy Spirit. Manicheism was quite popular, even gaining some adherents in the Roman Empire shortly before its decline. It rivaled with Christianity for quite some time.
Miaphysites and monophysites became distinct from the mainstream church (which would further divide into Catholics and Orthodoxs) following the Council of Chalcedon. All three had a disagreement over the nature of Jesus Christ: the Chalcedonian Church believed that Jesus had two distinct natures (an human and a divine nature) united as one person (think V + I = VI). Miaphysites believed that Jesus had an human and divine nature, but that they were not separate from each other and therefore compatible (as an analogy, the number 9 depicted in red is red, but it's still a nine). Monophysites believed that Jesus had a mix of an human and divine nature, held together as a single (not quite human, not quite divine) being (along the line of "5 is different from 4 or 6 but it's somewhere between the two"). Monophysitism was denounced as heretical, but the Chalcedonian Church was softer on the Miaphysites.
Samaritans do not consider themselves to be an heresy, but they have an historical rivalry with the Jews. Whereas Jews consider themselves to be the descendants of Judas (a son of Jacob, son of Isaac, son of Abraham), Samaritans believe they are descended from his younger half-brother, Joseph, born of Jacob's favorite wife. Both tribes were allied to each other as the Kingdom of Judas until it was conquered by the Babylonian Empire. The tribe of Judas was massively deported but Samaritans insist that the tribe of Joseph was not (or not completely). Separated from each other, the two tribes would develop religious differences on their own until the Persian Empire allowed the tribe of Judas (now called Jews) to rebuild their former kingdom (which they renamed Israel, because they believed that the other tribes were extinct). Samaritans were accused of mixing their religion with local paganism, which kind of explains the rivalry I mentionned earlier. Understandably, they refuse to be called Jewish, but insist that they are still Israelites (ie. descended from Jacob, also called Israel). They follow many of the same sacred texts as the Jews, but the textual errors between the Jewish and Samaritan versions are not the same (and the Christian versions tend to have textual errors on their own, though by comparing each version it's usually very easy to know where the errors are).
The Yazidi religion is mostly based on Islam, but might be related to Hinduism and Zoroastrianism. They believe that all Yazidi are descended from Adam, but not from Eve (I'd call it male parthenogenesis). For this reason, they are strictly endogamous and do not accept converts. They have three hereditary castes, and are not allowed to marry between castes. They believe that God is unique, but that he is served by seven main angels (which I assume are akind to the Amesha Spenta of Zoroastrianism), the chief among which they call the Peacock Angel. They revere the Peacock Angel as an example of moral perfection, but they have a story about him which is near-identical with one muslim story about Iblis/Shaytan. The story in question is about the Peacock Angel/Iblis refusing to bow to Adam. Muslims insist that Iblis was a d'jinn (not an angel) and that he was reprimanded by God for his refusal; Yazidis insist that he was, in fact, an angel and was complimented by God for having obeyed an earlier commandment about bowing to God alone. Understandably, they have a reputation for being devil-worshippers, though they make an explicit difference between reverence and worship, and do not consider the Peacock Angel/Devil to be evil.
That's about it for the ck2 heresies I know something about. If I let out a specific heresy that you want to know more about, I'm always willing to do the research for you and tell you what I find. Hopefully you don't find my post to be loaded with too much details.