Well, the YED told Sam in AHBL that Sam was his favourite because he John trained him well, he's smart, tough and most of all he's aware of the true nature of the world. A definite advantage over the other kids. We still don't know the exact nature of the YEDs plans, but I am sure we'll get to that sooner or later.

I am convinced that the powers are not harmless and that it is indeed playing with fire for Sam. We had 3 episodes with foreshadowing overtones already this season, in which good people turned to dark powers out of desperation and it always ended badly. There will be repercussions for Sam for using his powers, I am pretty sure of that.