There is only one Mega Thwomp in the game, found in Key Cavern. Unlike Spiked Thwomp, this Thwomp can't harm Link and will not fall down on him when he tries to walk under it. This Thwomp only blocks his way to the end of the dungeon.
Mega Thwomp is held at the top of the screen and will not budge until Link dashes into it with his Pegasus Boots. As the result, it will crack and fall into the floor, allowing Link to pass.
Four Swords Adventures
Mega Thwomps appear in the Tower of Winds and drop down from above in order to crush Link, unlike their Link's Awakening incarnations. Link will not be harmed by simply touching them, however, and can climb up them to reach other areas.