How to repair ~/Library permissions?

While migrating to Yosemite, I manually copied some ~/Library files and folders from my old system to my new system. Now some of the affected apps show weird behavior. Often they cannot save their preferences. One example is the iTunes error message when I try to backup my iPhone:

Whenever I check, my user has read & write permissions. Disk Utility Repair permissions unfortunately does not help here.

What are the correct permissions for files and folders in ~/Library and ~/Library/Preferences? And how do I set them?