If you don't consider the bug aspect of it, then it was probably the ability to travel between Beregar and Kazordoon using the Wagon System along with the Unlikely Pathfinder achievement. This discovery took 11 years and 4 months. The truth is, however, that this was only discovered due to a bug, and maybe if it wasn't for that bug it would still be a secret...
The Transmutator achievement has similar bug-related story, but in this case it was the opposite. It was bugged from the beginning and thus impossible to get, if it wasn't bugged it could have been discovered many years before. The discovery took 10 years and 6 months.
Leaving aside these discoveries shadowed by bugs, we get to the Fearless achievement. That one just takes a very, very long time, and it was discovered around 9 years after being introduced. The original discoverer did not reveal it, and it only became public knowledge 9 years and 3 months after the implementation.
Since Fearless took actually less than 9 years, we get to another achievement: The Snowman. It also took 9 years and 3 months, and is probably the mystery that took the longest to be discovered with bugs apart. Yet, the Beregar-Kazordoon connection should still probably get the "trophy" since it was never bugged, just really unknown.
You can read more details about all these discoveries here: Achievements that took many years to be discovered - TibiaLD