Synchronising Emacs configuration files between machines usually works well, but sometimes there need to be different settings for different operating system.

Thankfully, Emacs lisp provides the variable system-type.

For example, it can be used to set a different font depending on the os:

;; Windows only font
(when (string= "windows-nt" system-type)
  (set-face-font 'default "Consolas"))

;; Mac OS only font
(when (string= "darwin" system-type)
  (set-face-font 'default "Monaco"))
;; Linux only font
(when (string= "gnu/linux" system-type)
  (set-face-font 'default "Ubuntu"))

More info: Gnu Emacs: Operating System Environment