Wow to name one song... flat up can't do it. There are just too many amazing ones.
According to the play count on my iPod, the Pippen Song Magic track is the most listened to
One thing I can say is my favorite battle song (excluding Hymnos ones) is Indra, although all the battle bongs from the second are great. Didn't care much for the rap parts of the battle songs in the first game, songs were still great overall though. Battle songs from the third game to me all sound like chibi/upbeat stuff that remind me of the opening theme for Lucky Star... From hearing them, they don't seem suited for a battle situation at all, however my opinion may change once I hear them in context,
As far as Hymnos goes, I like it all save for 2 or 3 songs in each game, and the normal tracks are for the most part excellent as well.
I can say that the Ar Tonelico trilogy has by far the best game soundtrack I have ever heard, and I doubt any other games will ever be released that will have a score as beautiful, unique, and breathtaking as the Ar Tonelico series.