Ai-chan loves "The Heart Speaks", "Exec Harmonius" and "Hartes Ciel, Melenas Walasye" the most. But if we're talking about the whole franchise, that would include "Ode To An Unborn Star". You? Ai-chan always cries listening to these songs.
Did you play the game or got interested because of recommendation? It has more feel if you understand the setting of these songs.
In Ar Tonelico 1, the story is about pollution and the boss is a war machine who once loved mankind but was forced by her creators (humans) to kill other humans and a goddess who's so human that she's couldn't be relied on.
In Ar Tonelico 2, the story is about overpopulation and the wishes to create new lands to support the growing populace. Here the same war machine from Ar Tonelico 1 calls the goddess here as mad for refusing to allow new lands being made and forcing such poor conditions. The made the lands anyway and end up destroying a section of their world.
In Ar Tonelico 3, the story is about preventing the destruction of the planet. In this game, if you fail to save the planet, the other two towers from both AT 1 and AT 2 would die as well. Exec Cosmoflips is from this game