Indie games are the best example of well written games. The Chzo mythos, Facade, Immortal Defense, the girl who runs Amaranth games has some alright stuff going on, CAVE STORY, the Path. I could go on~

Even the breadth of topics covered by indie games is extensive ... the Path and the recent winner of an Adult/Educational games competition (Edmund) are about rape ... they're both really smurfed up games. I think the Path handles the subject matter better, though ... Edmund was just really, really disturbing (and it was 2D sprites o_O)

edit: Oh, and non-indie-wise - the Syberia series is by far the best storyline I've ever played through.