A cool, fancy way of saying, "I could tell you about this, but I won't because it's not really that related to what I'm telling you about now." Used quite often in the book, "The Neverending Story", and also in the movies based off of it and the cartoon series based off of the movies. It's basically one of those phrases that everyone yearns to find a good opportunity to say, like "I could tell you, but then I'd have to kill you", or "I'll be back...WITH WEAPONS!"
Once upon a time there was a thirteen-year-old who was bored so she decided to write a definition of "but that's another story for another time" on urbandictionary.com. After that she went on to do something completely different, with nothing to do in any way, shape, or form with urbandictionary.com...but that's another story for another time.