So, I've gotten to a point where my tool is basically finished, but there's bound to be small tweaks to do here and there.
You open it by going into NGUI->Open->Nicki's Draw Call Toolbox.
This is how it looks:

You can set the depth on Panels and groups of widgets that have the same depth. If you need to seperate an individual widget, you should expand the widget thingie and click the individual widget to go to it in the inspector, and change that there. I ran into som small issues with doing that directly in the tool easily, so that's not in yet.
The colors are set by Panel. That means that all that have the same colors are drawn by the same panel - so if you see something with the same color and same material in multiple places, that could probably be collapsed by moving the depths closer together.
When the numbers are changed, two buttons appear "Apply depth, Reset depth". Doing it instantly while typing caused too many problems with depths with more than 1 digit.
You install it by just putting the attached script into a Editor folder (doesn't matter where). I've decoupled it as much as possible from the rest of the NGUI core, so I don't stumble on side effects (DrawHeader set the GUI.backgroundColor to white, for instance), but I do still use the NGUIEditorTools.BeginContents/EndContents and NGUITools.GetHierarchy.
When you fold a draw call together it works as it does in the individual panels, and it does overlap with those - so if you fold it in the panel, or in my tool the others fold as well.
In this tool, when a draw call is folded, it turns bright red, to indicate that this should only be a temporary state and you should fold it back out again - they will stay folded together until you unfold them, so if you think you have missing references, that might be it.
Anyways, hope you can use it.
Updated link 15th jun 2014 http://nickithansen.dk/stuff/drawcalltoolbox.unitypackage (Unity 4.5+, NGUI 3.6.4+, no guarantees below that)