If you are using DropShadowsEffects, try assigning ones to the nodes' Adorner objects. Otherwise you might run the custom drawing code for a second time with slight offset and in a different color to draw shadows.

I hope that helps,
Stoyan

Selection handles are drawn in a separate visual object placed over the node, called Adorner. So you can add shadows to the handles like this:

node.Adorner.Effect = new DropShadowEffect();

Or the other method is if you call something like DrawRect(brush, x, y, 10, 10) to draw a custom handle, then before it call DrawRect(shbrush, x + shadowOffset, y + shadowOffset, 10, 10) to draw its shadow, perhaps using some semitransparent grayish brush.

I hope that helps,
Stoyan