QMC stands for QlikView Management Console while QEMC stands for QlikView Enterprise Management Console. These are the management interfaces to control QlikView Server and Publisher, add tasks, users, licenses, permissions...
They have been coexisting for some time until version 11, where there is only one Management Console (QMC). Anyway, if you are using versions 9 or 10, use always QEMC should you have to change any setting in the Server.
Hope that helps.