Five minutes into Jonas Kyratzes new browser game, Traitor, I thought I'd seen everything I needed to see and was ready to move on to something else. I'm glad I didn't because what seemed to be a basic space-based shoot 'em up that's making a fairly obvious comment on a player's readiness to obey commands ("Shoot these unarmed ships immediately!" "I'd rather not." GASP) turns out to be something more complicated and far more entertaining. Once what I now think of as the prologue missions are done, Traitor opens up and provides choices which lead to a series of complex little stories.
It's a little plodding considering the number of spaceships blasting one another but it weaves a very good yarn and shows the benefit of taking a simple formula and adding layers of story to it.
While you're at Jonas' page also check out The Infinite Ocean, an adventure which Quinns called "a deliciously dark slice of future-terror". There's also Phenomenon 32, described as a "2D exploration/platforming game with RPG elements". It can be a hard sell, despite being free, because it doesn't look like very much of interest is going on but it handles its superb alternate history plot just about as well as any game I've ever played. Here's a really old trailer.
I spotted Traitor over yonder at Indiegames.com.