Secret 1: Ifound69diamond's Secret Pillar Hideout
Discovered by Ifound69diamonds

How to get there: That boat by your starting point? It was not just for looks. Take a ride and head south for a while, and you should faintly see some glass in the water. Head down for the challenge!
Secret 2: The Pyramid of Distant Reaches
Discovered by TheDarkFlame

How to get there: Again, the boat serves further use. Sail further out to the land southbound to find this Pyramid. It's the grey part on your map. Solve the puzzles for a great prize! (You don't need the boat for any more secrets)
Secret 3: Trials of Torture
Discovered by Light671823(Yogscast Forum)

That Flint and Tinder does more than you think. Once your adventure is done, return to the town hall and you'll notice that indeed, the floor has red wool. Burn it and underneath some straight-forward(pun intended) trials await. But be careful! You get but one shot at it.. Also, be careful not to burn the town hall!
Secret 4: Underwater Treasure
Discovered by Light671823(Yogscast Forum)

Treasure waits for ye' near the snow. Travel beyond the area of the your Descent and you will find a small snowy market. With Flint and Tinder, burn the red wool to find underwater secrets!
Secret 5: A Haunted Grave...
Discovered by GravelLord

You were given the power to break loose Stone Slabs along your quest, but it seemed only useful in that area. Think again! Return to the graveyard and the oldest gravestone of them all lies in wait. Break it's Rock and descend below to uncover the secrets.
Secret 6:
Currently Undiscovered.
Secret 7:
Currently Undiscovered.