Pac Man; hand down
seriously, though - the (1st)
Disgaea (PS2) game had a great story (in a light-hearted, quirky, fun, charming, and humorous kind of way),
and for more mature/serious kinds of stories I'd list
Shadow Hearts 1 & 2 (PS2); moreso the 2nd game --but-- there is a bit of carry-over + there's
Koudelka (PS1) as a loosely-associated prequel to it; there's also a
Shadow Hearts: (3)/From the New World (PS2) game that - while, IMO, still being fun for the SH gameplay, doesn't come close to the 1st 2 games, story-wise,
and, to top off my 'top-of-my-head' List; I'd have to say that both
Vandal Hearts 1 & 2, on the
PS1 are excellent. Again, there's a 3rd
VH game - that I believe is only available digitally & from PSN for the
PS3 that; like
SH has some fun/similar gameplay & aspects from the original 2 but can't hold a candle to them storywise, either
my 'newest' favorite story (and OST) is
Tears to Tiara 2: Heir of the Overlord (PS3) which is only voiced in Japanese with English subs, though -
and - I'll close with two games that I haven't played yet (but I have them, want to play them, and will do so...eventually) that I've heard a lot of love for their stories are
999 (on the DS) and its follow-up
Zero Escape (which is on both the
Vita +, iirc, PSTV compatible (my own personal, definite preference & way I'll be playing it:) *but* if you don't have a
Vita...it's also available for the 3-DS.
*
almost forgot* to mention:
Wizardry: Tale of the Forsaken Land (PS2) which, is surprisingly, a far better story than the usual stories that come with dungeon-crawlers,
and there's always
Xenosaga (3 games on the PS2) - if you're into epic (loooong) stories with most exposition coming from FMV's / cut-scenes...that'll keep ya' busy for awhile
Happy Trails