Coming from a Linux/command line background, I prefer an all lowercase filesystem structure and so, based on Can I safely rename all directories in my home directory to lower case? and after confirming my filesystem is case insensitive in Disk Utility, I proceeded to rename everything in my home directory to lowercase.
One repercussion (there maybe others besides) is Alfred forgets his preferences. Having ran through Persisting Alfred's Preferences a few times, I ruled out permission issues. However, running AppDelete on Alfred Preferences.app showed references to the plist files with ~/Library prefixes (capital L). Renaming ~/library back to ~/Library solved the issue, which leads me to believe preferences assume case sensitivity.
Note, I haven't the OS X experience to know whether this applies to all apps, though Bryson in the AskDifferent thread linked above remarks
Alfred v2.0.4 (199)
OS X v10.8.3