I often see trees that have a single root item at Level 1. This root item is one parent from which the entire tree is descended (in the example below this is “Acme-MSU”). Because it’s there, all the other items in the tree are indented an extra 20 pixels. In any tree control the horizontal real estate is at a premium – tossing 30 pixels away for nothing is pointless.
Here’s another example – “System Management” has no peers in this tree, and it’s already shown as selected in the tabs on the left, so it’s completely unnecessary in the tree. (But don’t get me started on those tabs, please – they’re terrible).
To me, all this does is waste space. Take it out of the tree! If you really need some sort of master root label, then just add it as text above and outside the tree control.