Well if I had to whittle all of the songs just down to three I'd have to say third place would go to the Regi's Battle music because the syncopated notes and awesome bass gives you a thrill while battling. Second would be the Sevii Isle theme just due to the nostalgia it gives off and the new instruments introduced as well, making it a personal favorite. Final my most favorite song of third gen would have to be the Abandon Ship music from R/S/E. I'm just a sap for song with a sense of distress and sorrow.
Close follow-ups were; Mt. Pyre (Peak), Pallet Town, and the R/S/E Champion theme.