#NeXT / #Apple had the right idea.
-
User homes are in /Users
-
Each app is in /Applications and looks like a regular file but is actually a folder (i.e. you can cd into it and examine the contents)
-
The operating system is in /System
-
Files shared among apps (except files that come with the OS), including configuration files, are in /Library
-
Static libraries, debug info, C headers, OS API reference docs, etc go in /Developer