Final Fantasy IV
This right here is the eponymous JRPG - my first traditional game in the genre, my first Final Fantasy, on and on and on. THis is where it started for me, engendering an affection for games I otherwise may have never touched.
It is worth noting, here, that I am not simply putting this here out of nostalgia - the DS version of this game is brutal, long, and deeply strategic. It's the perfect traditional Final Fantasy, taking itself just seriously enough that its elements of tragedy are properly communicated. The plot is simple enough (in a way), but the particular elements of the story, especially the characters, stand easily on their own. Kain is the star of the show, the original "Final Fantasy bad ass son of a bitch" who begat such characters as Shadow and Auron, and greater than any that came after him. His internal conflict is indicative of the larger conflicts in the game, the problem of the evil within people struggling against their goodness, and his resolution is nothing short of perfect.
Thematically Final Fantasy IV is the tightest and most well-constructed game in the series, and I tend to tune out anyone who tries to claim otherwise. This game right here. Man. And the music! The music.
This is also the part of the list - the top twenty - where each game could be argued to be the best ever. Past here, ordering is almost arbitrary and immensely cruel. Anyone who called FFIV the best game of all time would get my support.