Absolutely "Don't Be Afraid" from FFVIII:
I think partially because it feels like it'd be a perfect Shadow of the Colossus song. I think Kow Otani may have learned a thing or two from Nobuo...
But, truth be told, I think Yasunori Mitsuda was always a little better overall than Nobuo. This is "Time's Scar", the opening song for Chrono Cross, and it gives me chills every time. Now I just want to fucking play that game again. His stuff tends to have kind of a... Celtic influence, I guess? That I really, really like.
(Make sure you switch the quality to HD since the lower settings cut out a bunch of the high end.)