When I think of grouping the icons for applications, I tend to think of groups with groups inside them.  But Fences 0.96.1650 acts up when I put fences on top of each other and that really isn't what I wanted.  If I put one fence inside another, Fences tends to stop seeing the inner fence.  That fence manages its icons properly, but won't respond to the mouse except for resizing the border.  I can click the icons, but if I want to rearrange, I have to move the parent fence out of the way.

I also should note that Fences can't organize icons for the parent fence if there is a child in the way.  The parent's icons will use the same space as the child.