Coded Myth refers to the notion that classical works of mythology or religion may have secrets encoded within them. The goofy stories of lusty Gods may have meanings that go beyond symbolism and into the arena of cryptography. Depending on which field of Alternative Science you use to approach this concept there may be great variation in what, how, why and by whom such secrets were encoded. Here's a few examples:
- Isaac Newton and George Starkey both felt that many classical myths were actually concealed alchemical recipes. For a specific example, see The Net (substance). The ancient Greco-Roman mysteries and many Western Mystery Traditions do indeed feature tiered knowledge, where parable or puzzle is presented to the student, and the true meaning of the story is revealed later by the masters. 
- In Where Troy Once Stood, Iman Wilkens proposes two separate theories. The first part is that the works of Homer were actually Celtic or Protoceltic, not originally from Greece. In the second part of the book, he charts the voyage of Odysseus, using Homers statements of direction and sailing durations. If the starting point is roughly Cambridge, England instead of Hissarlik, Turkey, the directions work and are quite interesting. For example, you arrive at an active volcanic island at the point in the voyage where Odysseus used fire on the cyclops's single giant eye (thus making it a crater?). 
- The Bible Code that some say has predictions about the future hidden in letter strings of the Torah.  Some Jewish mystics believe that the Torah contains hidden meanings deeper than the obvious commands, that every word and grammatical symbol is a potential revelation based on its position in the text. One kabbalistic interpretation states that the whole of the Torah constitutes one very long name of God, broken up into words so as to be more comprehensible to man. Again, Isaac Newton pops up - while the modern concept of bible code is unlike anything Newton found, he did believe that Sacred Geometry and other deep secrets were hidden in the bible. 
- Jesus Christ in comparative mythology and Christ Myth Theory. The three wise men may be a coded reference to the stars in the belt of Orion, and other elements of Jesus' life have parallels and resonances to various myths from a variety of cultures.  For that matter, Jesus did speak in parable quite frequently, similar to those Greco-Roman mysteries.
- The Da Vinci Code and the mystery of Rennes-Le-Chateau, which suggest that coded messages, religious revelations, and illuminated secrets are hidden in the paintings of the Old Masters.  
- Noted Atlantologist and one-time Lieutenant Governor of Minnesota Ignatius L. Donnelly also believed that the works of William Shakespeare contained a code that would reveal its true author. HINT: The words "by Wm. Shakespeare" on the flyleaf were not part of the code.
- British scientist uncovers 'secret messages' hidden in Plato's ancient text - the works of Plato contain hidden musical references, as well as Pythagorean numerical messages.
- Some refernces to homonculi in alchemical texts may be coded myth - either using human transformation as an allegory for the refinement of metals, or using the refinement of metals as an allegory for human transformation.
Game and Story Use
- In a skeptical low-fantasy campaign, codes such as this may prove to be just a case of Confirmation Bias or the Texas Sharpshooter Fallacy. There is no conspiracy or higher meaning, it's just people fooling themselves into seeing something that doesn't exist.
- More fun, however, might be a setting where these things prove true. Dark secrets are hidden just beneath the surface, awaiting critical thinking, a daring archaeologist, or a glamour failure to unveil them.
- A fun character concept might be an alchemist or wizard who draws his magic or illumination from an unusual source. Say, sorcery unlocked via the memorization of Shakespeare or L. Frank Baum.
- All this secret knowledge encoded in our myths may be the work of Ancient Astronauts or a Secret Society of Prehistoric Witches or refugees from Atlantis. It gives them a cover story, so they're library of myth they and their descendants study won't stand out as magic or valuable.
- As is the case with Wilkens' theories about Homer, other ancient writings could have coded treasure maps to resources, secret druidic enclaves and safe houses, etc.
- Perhaps they are also Time Travelers, and have developed this body of coded myth, mnemonic devices and bardic tradition so that they don't have to bring repair manuals with them into the past. Should a time machine break down anywhen in the past 5000 years, the Veteran Chrononaut just visits a temple or library to brush up on the mythic tales that reveal the information needed to survive in any era.
- Colors the way you look at mythology, eh? What secret meaning might be hidden in your favorite tale? Time to Reverse engineer yourself a fun campaign concept. What does your favorite mythological character represent?