Tough call.
I guess the game that made the longest-lasting impression on my nerdy life was Ys Book I & II. The ending never fails to bring a tear to my eye, since I'm a nostalgic wuss.
But Final Fantasy X made an even stronger impression in a lot of ways when I played it as an adult nerd and probably had an even more significant impact, just sans the nostalgic "when I was thirteen" stuff.
But FFX could've been improved in some ways, and surely I should try to be a bit "objective" in my decision here. And speaking objectively, Ocarina of Time is the closest a game has come to "perfection" in my view.
But as much as I love Ocarina, I've only bothered to play through it like twice, and surely replay value and time spent with a game should be major factors in this decision. I played through Star Ocean 2 no fewer than four million times, devoting a good billion hours to it.
But I haven't picked up SO2 in ages, and I'm a man of the moment. And the game that I've had the most fun with recently is Violent Soldier. Or is it Sinistron? See, there's the problem. The two versions are different enough that I can't consider them one and the same, and the rules of this topic clearly state that I must select a single title, "PERIOD."
So I choose Tenshi no Uta.