The Stone of Agony has been replaced with the Shard of Agony in Ocarina of Time 3D

If you collected twenty Gold Skulltula Tokens in Ocarina of Time 64 you could obtain the Stone of Agony. This item would make the Rumble Pak vibrate when Link was near a hidden secret. The 3DS does not support a rumble feature though, so the Stone of Agony is gone. But fear not! It has been replaced with the Shard of Agony, which operates in much the same way. But instead of your 3DS vibrating, you simply receive audio and visual cues of nearby secrets when you’re in possession of the shard.