Metroid, the back story behind samus is great and there is enough lore spanning all the games even the crap ones to make her complete from A to Z, leaving the rest of the universe open - fanfic, homebrew games, etc... are easily adaptable given the amount of information readily available.
However, my two most preferred are specifically: Final Fantasy 3 (usa - 6 in J.) and Chrono Trigger (snes - didnt much care for the added content of the DS version)
In Final Fantasy 3 you cover so many different characters, their individual back stories and how they all came to meet and what role they play in the epic story.
My first time through the game took me nearly a year to complete (im a perfectionist and i tend to xp grind WAY TOO much
)
but the story and detail to every character and the lore behind the story`s events itself was just inspiring - back when making a game was about plot and character development, solving puzzles, strategy and actual thought process/imagination - graphics, audio and bell and whistles came second - ah substance... rest in peace....
speaking of substance: that`s where Chrono Trigger Ties up the race. a simple kid, tossed into a crazy life/world altering events by sheer random chance.... (*cough destiny cough*) and finds himself chasing and courting a princess, fighting demons, demi-gods, TIME, and all manner of monsters and evil. In the year 1000 a freak accident rips a hole in space and time and sends him and his friends 400 years into the past, where a plot of treason and betrayal risk to undo all they know from their time. Solving that one issue leads them from their "present" (yr1000) to the year 2300 a post apocalyptic place of ruin, to the dawn of humanity in 65,000,000 BC - even to the very end of time...
Multiple endings, no linear story, wicked crazy plot development - one of few games in which the main hero is killed off LOL Come on - how is it no one called these two before me?