Why does Jack put clay on his face, and what is its effect in Lord of the Flies?

Jack puts paint on his face, literally, to help him hide
in the bushes as he hunts for pigs.  It is camouflage.  Figuratively, Jack puts the
paint on his face to hide his true identity as a civilized human.  The painting of his
face is like putting on a mask to hide the part of Jack that used to function in
society.  The effect is that Jack is able to let more of his uncivilized side out and he
becomes wilder and more vicious.

Roger throws stones at the
littluns, Henry in particular.  Roger does not hit Henry; he misses him on purpose.  The
reason is that Roger still has some vestige of civilization left in him, "Here,
invisible, yet strong, was the taboo of the old life."  The civilized part of Roger
keeps his arm from doing what he has been conditioned not to do - to hurt someone.  This
scene serves as sharp contrast to the scene later in the story, when Roger pushes the
boulder onto Piggy, killing Piggy.