Aside from the clustering, which no doubt you guys are already onto, a thought of a tool which would be nice when dealing with larger scenes:
Distribution of nodes, ie.
- Align horizontal
Align vertical
Distribute horizontal
Distribute vertical
And perhaps even (though probably not) snap to grid?
CamN
Octane for Rhino | Windows 8.1 x64 | i7-3820 OC | GTX970 4GB OC & GTX 560 Ti 1GB OC | 32GB DDR3