There are six Harmony Stones that need to be activated in order to defeat Nightmare Moon. Harmony Shards are used to activate the Harmony Stones, but the Harmony Stones also need to be brought out of the Darkness first.
The Laughter Stone is the easiest to activate, and the Magic Stone is the hardest.
After a Harmony Stone is activated, excess shards can be used on the Harmony Stone to produce extra Bits.
Laughter Stone (requires 25 Laughter Shards): Slightly south-east of Twilight's Library.
Honesty Stone (requires 50 Honesty Shards): South and slightly east of Twilight's Library.
Generosity Stone (requires 75 Generosity Shards): East and slightly south of Twilight's Library.
Kindness Stone (requires 100 Kindness Shards): Slightly east of Laughter Stone.
Loyalty Stone (requires 125 Loyalty Shards): South of Twilight's Library.
Magic Stone (requires 150 Magic Shards): The south-west corner of the map.