If Greninja has Splash Energy attached and is Knocked Out by damage from my opponent's attack, do I put the Greninja card into my hand or to the Discard Pile?
No, you put all the Pokemon in the evolution line into your hand, including Mega and Break evolutions. Any other cards attached such as Tools or Energy are discarded.
Source: BREAKpoint FAQ (2016-01-23), TPCi Rules Team (2016-02-11)

Relevant cards

Note: All applicable cards may not be listed below.
XY9_113