You're right, the auto-wire-organizer tool is fantastic. Every time I use it I wonder what algorithm LabVIEW is using to rearrange things - not an easy problem computationally I'm sure. I use it for small sub-VIs but I find that if I use it on a large project I can't find anything after using it - I was relying on spatial layout of the VI which was lost after auto-formatting.

I guess this is analogous to algorithmically reformatting code in a normal text-based programming language...