I've been playing around with the idea of a Thassilonian runic alphabet that I could write messages in to represent scrolls, etchings or notes that the PC's might come across. I wanted them to have fun decoding them as they learned more and more of Thassilonian culture.
I started with the Masonic or Pigpen cipher which would be challenging enough for those unfamiliar with it, but once solved it was too easily applied, and for those already familiar with it out-of-character, the novelty would wear thin quickly. So I made a few modifications of it...
First I had Thassilonion write vertically, top to bottom. then I added a Circle and a Circle with a dot into it, the first to represent the spaces between words and the second to represent the spaces between sentences, allowing you to run-on with your text. Those adjustments were nice, but I wanted to add something that really put some 'oomph' to it and added depth to the ancient empire.
That's when I realized that the two 'tic-tac-toe' & two X's could actually be re-arranged into six different combinations (as opposed than the standard + + x x), and that in each one the cypher would result in very different decoding. It occurred to me that in ancient Thassilonia they might have used different 'alphabets' depending on the purpose of the text being written. One configuration might be used for poetry, another for official governmental text, one for military purposes, one for history, one for religious writings and the sixth could be reserved for casual or every-day use. I'm actually not settled on the various categories of writing but it seemed like it would make for a really interesting curveball... that, and determining that there was something unique and inherent in Thassilonian script that prevented it from being decipherable via magic (like Comprehend Languages).
I'm going to use this concept in the new campaign we have starting up soon. I'll let you know how it goes if there's any interest. I figure I can write text in marker on the brown paper of a paper bag, crinkle it up and then flatten it out before tearing the edges off. Should make for a nice hand-out, no?
EDIT: I'm actually thinking of replacing the 'dot' with a second vertical line in the case of characters cyphered by the tic-tac-toe frame and a second diagonal line for the ones cyphered by 'X's. That should throw even those familiar with the original cypher for a loop.
EDIT 2: Perhaps those additional lines (replacing the dots) can carry some meaning as well. for instance, if the writer is male, he might add an additional vertical line / left to right diagonal and if the writer is female she could add an additional horizontal line / right to left diagonal instead. The same character would carry different meanings depending on the sex (or perhaps social status?) of the writer as well as varying within the different castes of society as mentioned above.