Thousand Dollar Soul
A sci-fi story that is deeper (and creepier) than it first appears. You'll have to play through several of the 35 endings to piece the whole picture together. The interface allows you to back up as much as you want.
A visual novel about a relationship with a needy friend. Or is it?
An interactive zombie survival movie. It has the usual limitations of interactive movies, plus horror movie clichés, but does some clever things with a few branches, and dying is as fun as winning.
Dead Frontier: Outbreak
Dead Frontier: Outbreak 2
Two zombie apocalypse choose-your-own-adventures, with music, voice-over, and background graphics. Click to skip through text.
Choice of Dragon
Choice of Broadsides
Choice of Romance
Choice of the Vampire
These are the best written on this list, and mechanically interesting as well. Each game tracks attributes for your character's choices, and the story changes based on your attributes, sometimes in substantial ways. While I'm not usually a fan of the genres they chose, all but Vampire got me hooked. It is in itself notable for the broad scope it attempts, though it ultimately fell short of a good story, in my opinion.