There are also those that refer to themselves as Side Quests, but are better described as Mini-Questlines set in self contained mini-maps with their own unique Plots and Quests. Most but not all have a unique Weapon as the final reward for completion.
These will appear as you advance through the game, most need you to unlock certain maps and go looking for new areas opened up, while others will simply activate like any other Side Quest.
Listed below are all the Special Areas in order of discovery:
While not technically a secret area with it's own mini-map, it deserves a honourary mention for what exactly it is and what happens there. You need to reach Level 6 to open the teleporter in the Haven Castle Courtyard, but once open it can be fast traveled to from anywhere.
'A Fateful Balloon Ride...' Edit
Entered by reaching the Harbour and heading through the upper gate, this will be the first Special Area you gain access to at the earliest when reaching Level 16.
'The Buried Pyramid' Edit
The second proper Special Area can be accessed at the ealiest of Level 32, after giving a Jade to the Left gate guard in the Dusty Wastes, then heading down through the already open gate and clicking on the crashed ship.
'Skull Island' Edit
Reached via a rowboat in the Map Zone the Deserted Island on the most southern tip of the island chain. The island chain itself cannot be reached until you hit at least level 40.
'The Snowy Crater' Edit
The arrow points to the field that holds the entrance to this hidden realm, but you will need to reach level 60 to gain access to it.
'The Rabbit Hole'Edit
The starting quest only appear once Level 70 is reached, and is given by Sasha standing next to the Statue outside Haven Castle.
(More to be added as they are reached)