Two questions, really:
Is there a standard/convention regarding the placement on configuration files?
For system or quasi-system programs they see
(1) No (unfortunately). Edit: The other answers are right, per-user configuration is usually stored in dot-files or dot-directories in the users home directory. Anything above user level often is a lot of guesswork.
(2) System-wide ini file -> user ini file -> environment -> command line options (going from lowest to highest precedence)