The immortal Emperor of mankind is an amalgamation of every heroic leader from fiction, history and legend; Gilgamesh, King Arthur, Caeser, Constantine, Jesus and Paul Atredies to name a few. King Arthur and Paul Atredies are two of the stronger influences.
King Arthur was a man that became leader of a nation through a form of divine right. Only the true king of England could pull the sword from the stone or show his true form as the Emperor did. He then goes on to reunite England (the galaxy) and surround himself with the best of the best; the Knights of the Round Table (the Primarchs and their legions). They laugh, they cry, they go on a quest to find the Holy Grail (uniting humanity and searching for Dark Age technology). Eventually he is mortally wounded by his son Mordred (Horus) and taken to Avalon (the golden throne).
Dune, one of the most influential pieces of literature for 40k, gives us Paul Atredies. The Kwisatz Haderach, as Paul is known, is the ultimate human or the �One�. Much like the Emperor he knows what destiny demands of him, the uniting of the universe.
The Sisters of Battle have several sources, with the largest being a single person. The French saint Joan of Arc, about the closest thing you�ll find to a female warrior monk in the European history. She was an extremely pious woman and this is seen in the religious feel to the army. Another French connection to our peasant girl is the fleur-de-lis, symbol of France.
Before the Black Templars came into being, the SoB filled the roll of zealot warrior monks, much like the Knights Templar. Also from history the Scythians, to whom the Amazons belonged, are an example of an all female army. Our ancient attitude to flame comes in to make up of the SoB in that flame was always thought of as a purifier.
Seraphim take their name from the angels of the first order, usually portrayed as the winged head of a child, in Christian mythology. The special characters backgrounds are an interesting mix. Inquisitor Lord Fyodor Karamazov�s name is from the novel �The Brothers Karamazov� written by Fyodor Dostoevsky, a book about a pious young man; Alexei Fyodorovich Karamazov. The Inquisitor�s opponent Ecclesiarch Decius XXIII may be named for Decius, a Roman emperor known for his severe persecution of Christians. This leaves the Salem Proctor which most likely is a reference to Salem Massachusetts and its witchcraft trials of 1692. Now the living saint, Celestine, has a name that means heavenly and had fought during the Palatine Schism. Palatine is the most important of the Seven Hills of Rome and supposedly the location of the first settlement and the site of many imperial palaces.
Translated, it means the order of the hammer. Since the Ordos Hereticus and Xenos have a straight forward basis for their names, why use Ordo Malleus? It is taken from a book first published in 1486 called the Malleus Maleficarum or the Witch Hammer; a how to book on witch hunting. This ties in with the hammer symbol of the order.
The one special character with a historical reference is Torquemada Coteaz who is loosely based on the real life Tom�s de Torquemada, a Spanish inquisitor.
ADEPTUS MECHANICUS
The adepts of the mechanical would be a decent interpretation of their name. They may be based on how, after the fall of the Roman Empire, knowledge was gathered and preserved in small, isolated communities of priests and monks during a centuries-long dark age. This is seen in the novel �A Canticle for Leibowitz� by Walter M. Miller�s. However Isaac Asimov's �Foundation� series is far more influential. A galactic empire on the verge of collapse sends a group of scientists, the Foundation, to a remote planet to work on the Encyclopaedia Galactica. Within fifty years the empire has lost control of the outer systems including the sector containing the Foundation. To protect themselves the Foundation sets up a religion around science and helps its neighbours. The priests, who wear red robes, of this religion believe in a mystified version of science, one even going as far as to curse a ship which leads to its loss of all power. The Encyclopaedia Galactica from the book is the sum of all human knowledge and is implied that it contains schematics and other information similar to the STC.
Another source may be the medieval guilds of Europe who had control over processes and methods of manufacture. This control allowed a select group of people to have access to this information. While this is very much like the Adeptus Mechanicus, the way apprentices learned bit by bit with information held back is even more so. The products created by guilds eventually would give a city/region a reputation for quality goods (eg. Champagne or Damascus steel). The Forge Worlds also strive for these reputations and many weapons and vehicles have a pattern named for the world of origin. In the end the guilds were to be accused of what the Adeptus has become, hinders of technological innovation and knowledge transfer.
The military might of the machine cult starts with the Titans, who are named for their Greek mythological counter parts and are commanded by a Princeps and his Moderatus. Princep is Latin for first citizen and Moderatus possibly is derived from modus operandi or mode of operation, as these people are the ones who operate the titan. The Knights follow their medieval counter parts only in a cockpit not on horseback. This leaves the Skitarii who may take their name from a group of Byzantine infantry, called Skutatoi or Skoutatoi. The Byzantines relegated infantry to a secondary position of importance to the cavalry soldier. Cavalry in this case can be seen as the titans.
The powerful houses of the Navis Nobilitae are taken directly from Dune and its navigator guild. While they don�t fold space, traversing the Warp is the next best thing.
The Callidus takes her name from a Latin word that means dextrous and sly while the Eversor is also Latin and means destroyer. The word vindicate has one meaning that is to defend, much like what the Vindicare does with his exitus; Latin for exit, rifle. Last the Culexus uses the animus speculum or mirror of hostility; as animus is a feeling of ill will arousing active hostility and a speculum is a mirror.
A mix of two elements may have been used to create the Rouge Traders. From history there is the privateer, best described as a state licenced pirate. Then in the book Foundation by Isaac Asimov we find the traders. A group not unlike the 40k Rouge Traders.