Try inserting this into your init file. It should make sure emacs saves files as Unicode (and reads them correctly afterwards).
;;;;;;;;;;;;;;;;;;;;
;;; set up unicode
(prefer-coding-system 'utf-8)
(set-default-coding-systems 'utf-8)
(set-terminal-coding-system 'utf-8)
(set-keyboard-coding-system 'utf-8)
(setq default-buffer-file-coding-system 'utf-8)
(setq x-select-request-type '(UTF8_STRING COMPOUND_TEXT TEXT STRING))
I'm fairly certain most of these options are unnecessary, but after inserting them I never had encoding problems again. Better safe than sorry. :-)