You could try what I do.
Bind the skeleton with a smooth bind, then start to move one side (sat the left) of the skeleton so you can see the dodgey areas. Select the dodgey verts either using standard selections or using the paint selection tools.
Then go to skin->edit smooth skin->Smooth skin weights, you should then see the verts go to where you should expect, if they dont quite get there smooth the skin weights again. To go back to the initial pose just select go to bind pose, then repeat with other joints.
When you get to the neck, I usualy select all the verts in the head then go to the componanat editor and then just add a value of 1 to the joint I want to control the head, this gives a bit of a strange look but just go the smooth skin weights again on te dodgey verts and it should be fine.
This works really well for the shoulder, spine and hip areas, but its not too good for the elbows, you'll have to paint them.
Once one side is sorted, mirror the weights over.
Hope it helps
"No pressure, no diamonds" Thomas Carlyle