Emmer Effer is the phrase used when it is not appropriate to say mother fucker. It is most likely used when something you do goes wrong or describing someone who is one crazy emmer effer.
Person #1: Did you see that girl do a keg stand for a whole minute?
Person #2: Hell yeah she is one crazy emmer effer!!
Person #1: Are you ready for the test today?
Person #2: Emmer Effer!!! I forgot all about that.