Since Einstein we know space-time is relative and more complex than we thought, and since 3D is not a challenge any more it looks like developers are trying to get the most out of these 4 dimensions. 
 
Time ago Link would travel back and forth in time to solve puzzles in Ocarina of Time, and   Blinx would claim to be a game in 4D. But those were to some extent isolated cases. Now the whole franchise of Portal, defies the whole continuum idea of space to solve puzzles, while what is up and down is not clear if it does even exist in And yet it moves. At the same time, if I may say so, TimeShift had some time manipulation, but this has been much more laureated for  Braid, which requires handling time in quite unique ways for puzzle solution, and Singularity, which takes this to a faster paced full retail action game to some extent, as when compared with downloadable puzzle games.
 
This is a new trend and my impression is that developers are just scratching the surface, most probably we will see a Braid 2 game in not too long time, and probably I forgot about many games in this short blog post, so feel free to correct me or add any other relevant titles, feedback is always welcome.