Actually as a new merchant I use the ! in front of my products runtime folders so they "float" to the top of the folder structure, making them easier to find and work with.
I dont always remove them because it can become a pain at the end of the packaging process.

As mentioned above I apply all sorts of markers to my runtime structure to again float favourite folders to the top of the file sturcture.
I would imagine most competent users would do this?...

I thought one of the cooler features of poser was the ability to rname and remake folder structures to assist in navigating through the mind numbing array of folders...