Dark, especially Season 3, is an interesting mishmash of themes. Destiny and true love collide with the science of nuclear energy and quantum mechanics, all wrapped up in a time-travel plot. Christianity is one of the most conspicuous motifs in the Netflix series. Numerous characters have biblical names or quote scripture in passing, and visual symbolism runs rampant throughout. Here's all the references you were curious about, and a couple you may have missed, throughout Dark's three seasons.
Spoilers ahead for all three seasons of Dark.
Biblical names in Dark
Jonas is the Greek variant of the name Jonah, a biblical figure who strayed from God's path and was swallowed by a whale to repent. The parallel may seem sparse, but in a way, Jonas is hesitant to follow the path he has to, one he knows leads to him becoming Adam.
Martha was one of two sisters in the New Testament whose home visited by Jesus. Her sister Mary sat at his feet and listened to him speak while Martha was busy with meal preparations. According to the Gospel of Luke, when she complained to Jesus he replied "you are worried and upset about many things, but only one thing is needed." This could symbolize Martha's worry and upset about her life and the things around her, but not the issue at hand: the God Particle and the end of the world.
Michael the Archangel is the warrior angel in Heaven: it's him who's the first line of defense against the work of the devil and other forces of evil. He's also sometime referred to as the Angel of Death. This is referenced in the way Michael Kahnwald's death kicks off the entire story.
Noah is obviously a reference to Noah's arc, and in a way he does serve as a sort of Noah figure, convincing nonbelievers that time travel is real. In Season 3, his name takes on a new meaning as he assists in "filling the gaps" and time hopping to acheive the goals of Sic Mundus across worlds: he's saving the world in pairs, but these pairs are alternate reality versions of each other.
Elisabeth was the cousin of the Virgin Mary and the mother of John the Baptist. Her role as the mother of her own mother, Charlotte, is a huge part of the plot of the show, but the most interesting parallel is a bit more obscure: in the Bible, Elisabeth's husband Zechariah is a priest who was struck mute by God. Noah, Elisabeth's Husband in Dark, was also a priest and broke Helge's silence with a bible verse.
Adam and Eva are pretty self-explanatory, from them (Jonas and Martha) spawns The Origin. The only difference is instead of life, he's the Origin of the time loops.
Scripture quotes in Dark
When something kills 33 of his sheep, Hermann quotes from Mark 13:33, "Be on guard! Be alert! You know not when that time will come!"
It's implied he got this quote from the new parish priest, later revealed to be Noah. This quote directly references the apocalypse, so it's ironic Noah would use it, considering he's one of the few characters who learns when the apocalypse happens in advance.
When Helge is returned basically unharmed, his mother Greta breaks into Scripture, she quotes Hebrews 4:13, which explains nothing is lost from God's sight. Later in that episode, Helge's first words draw from Psalm 119, about taking refuge in God. These verses aren't as applicable to the greater plot of the series, but ring true to what a religious woman and a priest would quote in those situations.
The number 33 in in Dark
In the aforementioned scene, Hermann quotes Mark 13:33 right after 33 of his sheep are killed. Seems like quite the coincidence, but it's far from that. The number 33 pops up constantly, most obviously in the cycles of time travel, always in 33 year chunks. H.G. Tannhaus, the creator of the time machine, explains to The Stranger, aka Adult Jonas, the biblical significance: Jesus performed 33 miracles, there are 33 litanies of the angels, Dante wrote 33 cantos for purgatory and paradise.
Jonas adds that 33 is the age the anti-Christ takes over, but forgets a major reference: 33 is supposedly the age Jesus was when he was crucified.
Breaking it down even further, 3 represents the Holy Trinity, and the number of worlds by the end of the series. It's Dark, everything is connected.
Biblical art and symbols in Dark
Peter Paul Rubens' The Fall of the Damned hangs in the Sic Mundus study, depicting Michael the Archangel banishing the fallen angels to Hell. This is very fitting considering Adam's past as Jonas, when his father Michael killed himself, turning his life upside down. It also fits Sic Mundus's determinism beliefs of pressing the apocalypse to happen.
Conversely, Cranach's Adam und Eva hangs in Eva's study, underlining the dichotomy between her and Adam, as well as her world compared with Jonas's world. These paintings are set on fire by The Unknown, perhaps foreshadowing Adam and Eva's own destruction. The alt-world's Sic Mundus counterpart, Erit Lux, is also a biblical reference: it's Latin for "let there be light."
The triquetra seen many times throughout the show is actually a Celtic symbol used in paganism, and for the logo for the TV show Charmed, but in Christianity is usually meant to represent the trinity. However, in Dark, it probably represents the "knot" formed by the three worlds: Jonas's world, Martha's world, and the Genesis world.
Saint medals are commonplace in Catholic communities, and are especially common given as gifts. This explains why this medal changes hands so often, crossing centuries. It's fitting, then, that St. Christopher is the patron saint of travelers and transportation. You often see medals like these hanging from rearview mirrors or clipped to visors: he's good to have on hand when you're going somewhere.
Legend has it, St. Christopher, who lived centuries after Christ, was asked to carry a young child across the river, who revealed himself to be Jesus. This is very compatible with the themes of Dark, when a young version of Jonas reveals himself to his older selves and other characters.
All three seasons of Dark are streaming on Netflix.