Foucault's Pendulum: This experiment was actually designed to prove the Earth's rotation. It is basically just a big pendulum that swings from a point suspended above the ground. As the Earth rotates, the plane of the swing seems to change (it makes these ellipses), but in reality, the plane of the swing doesn't move, the Earth moves under it, giving it the illusion of moving. At the poles, a full rotation in the plane of the swing takes 24 hours; everywhere else, it takes longer. Wikipedia has a nice animated gif about it.
The fixed point of reference seems to be treated with some special reverence in this first chapter, as it is a fixed point that in fixed with respect to...well, everything. Also, I suspect that it's featured because the pattern the swings make over the course of a full rotation draw out a rose pattern when viewed in time-lapse from directly overhead.
Atlantis and Mu: They are both fictional "lost continents" that sunk into the ocean. Sometimes Atlantis is identified as Mu. There was a theory that the people that fled the ruins of either/or continents migrated to other parts of the world and founded the Egyptians and the Mayans.
Agartha: A fictional city or country located at the Earth's core, with Shamballa or "Shangri-La" as its capital, supposedly located somewhere in Tibet or the Himalayas (although how it can be at the center of the world and in Tibet is anyone's guess. Maybe I'm just not enlightened enough to understand). It is ruled by the Masters, the keepers of all the world's secrets. The concept is popular in Vajrayāna Buddhism, also known as Tantric Buddhism. Supposedly, it was the location of the original Garden of Eden and all its wisdom will be shared with the world when we finally reach the state of purity in the Ten Commandments, "when the Anarchy which exists in our world is replaced by the Synarchy."
Avalon: The mythical island where King Arthur's sword Excalibur was forged and where he went to rest and sleep to recover from his wounds. Supposedly it was where Morgan le Fay, who seems like one of the woman druids, a sort of Celtic shaman figure who worshipped female Earth and fertility goddesses, and her sisters lived (some kind of druidic commune?). The story about how King Arthur never really died but is only sleeping and will one day return sounds an awful lot like the Jesus myth (someone suggests later in the book that the Jesus myth is stolen from Celtic legends). It has parallels with the Greek Hesperides, a mythical garden where beautiful women tended apples. Apples have something to do with Avalon, too.
Panta Rei: Apparently Eco just made up this secret society. Its name, in Greek, means "everything flows" -- as in, everything is connected, there are no coincidences, everything has a meaning. Also, a great band name, if it's not already taken.
EinsOf: Kind of a name for God, in his incomprehensible form, in Kabbalah. It literally means the "infinite," or the "nonexistent," in the sense that God is so far above human comprehension that it is as if he doesn't exist.
Armand Dufaux: a famous Swiss aviator, one of the first, who flew Lake Geneva.
Baal: It is actually sort of an honorific title in Hebrew, but somehow things got twisted along the way. Baals were the names of the little idols that people worshipped back in the day of polytheism, before Judaism with its one God thing became popular; when the Bible was being assembled, the Baals were confused for all referring to the same persona (false gods, all of them),
and became associated with a high ranking lord of Hell, even Satan himself.
Maiden of Nuremberg: a famous Iron Maiden, which was a torture device with pointy sharp things in it, used to force people to confess to heinous crimes like praying to the wrong piece of wood.
Francis Bacon, House of Solomon, New Atlantis: Francis Bacon was a philosopher and politician who is credited with inventing the scientific method. He did a lot of things. Somehow he found time to write this book called the New Atlantis, which describes a utopian society governed by knowledge and reason. The House of Solomon was his design for a modern university where people learned things and conducted experiments and stuff. However, he also describes a section of the university that features exhibits meant to confuse the senses, show illusions, falsehoods, which is what Causubon is equating the museum he is hiding in to.
Legion of Honor: The highest decoration in France, established by Napoleon.
Empedocles: a pre-Socratic Greek philosopher (apparently they were interested in finding a more reasonable explanation of how the world worked, and so wrote a lot about the essences of things) who wrote that the world was composed of four essential elements. He also believed in reincarcation. He supposedly died because he threw himself into a volcano, believing he would come back as a god afterwards. However, the volcano spit back one of his sandals, meaning that his body hadn't transcended after all, or something.
Alhazen: an Arab scientist who studied optics at the turn of the millenium, some people say he is the first real scientist. Long before Einstein, he was saying light had a finite speed and was made up of particles.
Demiurge: A Platonic concept for someone who is a kind of caretaker for the physical parts of creation, although not the supreme creator himself. The Gnostics, a bunch of mystics predating Christ who believed the Universe was created by an imperfect being who is either actually evil or is just imperfect, associate the God of the Hebrews with this Demiurge. According to them, there is an even higher God, an actual perfect Godhead, above this Demiurge. "Gnosis" means "to know," and it refers to someone achieving through mysticism and esoteric knowledge an understanding of eternity and creation and the perfection of the immaterial.
Basilides: an early Gnostic leader who is also associated with the origin of the Kabbalah.
Hermes Trismegistus: the blend of the Greek god Hermes and the Egyptian god Thoth (god of wisdom).
Notarikon: a method in the Kabbalah by which you take the first or last or whatever of a word and form new words out of it.
Yaldaboath: one of the Gnostic archons, the Demiurges who made the world but trapped man's essence in material form, with a lion's head and a serpent's body, sort of a demon.
Sophia: The all powerful all knowing mother-virgin-seat-of-all-mysteries goddess of the Gnostics. She was the good part of the "God", who wanted to create the world, and urged on the Demiurge, who, not able to correctly manipulate the base matter, trapped her inside the world.
Pleroma/ogdoades: the Gnostic word for the totality of all the divine powers. There is some concept of a heavenly pleroma, which is where all the divine beings live, and with the help of aeons like Jesus and Sophia, humans can reunite with these divines and learn their wisdom and the meaning of life. Or something like that.
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