Well-developed plot, fleshed-out characters..
Well, to list the games I consider to have a plot driven story, and or well a well written character dynamic:
I Love Daddy
Good Girl Gone Bad
Wicked Choices *This one is only at it's 4th release but its one of the best written stories I've played
Dreaming of Dana
My Sweet Neighbors
My Girlfriend's Amnesia *This one is an RPGM and it shouldn't be, but it has a great story so it makes the format bearable
Intimate Relations *This game is also pretty early in its development, but its made by Ptolemy who did Dreaming of Dana
Dual Family *This game has some depressing themes but I really enjoy it and think it's a refreshing take on incest
Those are the ones that stand out to me. I could give a few honorable mentions to some short but sweet games like:
My Legacy *I just like the main character and his motivations. The rest is pretty cookie cutter
Two Sides *This game starts out strong but there's not much content yet I hope to see it fulfill its potential
View Of Family *This game is a basic fuck'em'all like Big Brother, but I like the character models, there's no Eric, and the individual plots are fine. The grind is also pretty manageable.
SisterSisterSister *Honestly I think this was my first game after I started playing them. Its really simple but fun and does have a story that we are continuing to follow and learn.
Dreams of Desire *Like View of Family this uses the basic brother big sister little sister and mom format, only the added mind control element and the story that comes with it make it unique. I enjoy this game even if its mediocre.