Runes are used in the Deckathalon to craft the new Decks made for the Deckathalon, as well as some stitched wands that were also introduced with the Deckathalon. You can also craft a number of Treasure Cards using these runes at the end of a Deckathalon run, and only at the end of a Deckathalon run unfortunately. Check out Kara in the Library to see some of the recipes. Others will be made available by talking to her when she shows up at the end of a Deckathalon run. She has different recipes on each stage, so make sure you talk to her after you complete a stage for the first time.
Unfortunately by the time you may see this message, the current Deckathalon will be over and most of these runes will be unusable for the time being. The next one should occur sometime in late October.