One of the biggest indie games of recent years, Braid, made you manipulate time to complete platform puzzles. Unity-based browser game Stream also uses this idea, but in a first person 3D environment.
Using traditional mouse and keyboard controls for movement, time manipulation is shared between the two. This is my main criticism of the game, as it can be confusing. Despite this, Stream offers some complex but satisfying puzzling. The first levels are pretty simple, but the second floor puts you up against some daunting rooms to get through.
[via Indie Games]