My wife and I make it a point to pray daily over and with our kids.  Here are some of the scriptures we pray over them daily.

Oh, that you would bless our children and enlarge their territory! Let your hand be with them, and keep them from harm so that they will be free from pain

1 Chronicles 4:10

We pray that our children will be without any physical defect, handsome, showing aptitude for every kind of learning, well informed, quick to understand, and qualified to serve in the king’s palace

Daniel 1:4

The LORD bless our children and keep them; 
 the LORD make his face shine on them and be gracious to them; 
the LORD turn his face toward them and give them peace

Numbers 6:24-26