I'm assuming that you're using a graphical emacs, and not just using the OS X bundled version from within Terminal.
To ensure that Emacs responds to keystrokes in the same way as other OS X apps, try the following:
(setq default-input-method "MacOSX")
And in particular, if you want to use the Option key to enter extended characters not on your keyboard (e.g. "Option-c c" => "ç"), use these settings:
(setq mac-command-modifier 'meta)
(setq mac-option-modifier 'none)
(Put these commands in your ~/.emacs or ~/.emacs.d/init.el emacs startup file, and restart Emacs, or just "M-x eval-buffer" while editing the file.)