Edit: I was using the wrong terminology - I've edited this post to change "clips" to "loops"
Folders are one of Logic's best kept secrets. I use them to organize song sections. They work much better than the arrangement track when song sections overlap (for instance because of pickup notes).
I submitted the following feature request to Apple:
Loops within Folders:
When in a folder, the loops are disabled ("Double Click to return to the live loops grid"). It would be great if the loops workflow worked within folders as well as the top level of the project.
Folders within Loops:
Being able to store a folder in a loop would be a fantastic feature - this would effectively allow me to launch entire arrangements or song sections from the loops grid, e.g. verse, then chorus then bridge...