So my top choice is <span class="bold">Myst 3 Exile - Main Theme</span>.
If you open it up to licensed music composed for some other reason (say for a movie, rock songs, etc.) then my answer would be very different.
I don't speak Japanese, so I'm just judging it on a musical basis. I really like Yae's voice and the harmonies and arrangement are lovely. The English release of the game 'dubbed' these songs and the American singer uses far too much vibrato and doesn't pull off the harmonies nearly as well, I'd rather listen to beautiful singing that I don't understand.
As a bonus, here's the credits theme from the Japanese version: Starry Moonlit Night