One of the major difference between QMC & QEMC is that you can manage multiple instances of qlikview server using QEMC but not by using QMC & also there are sevral settings & configuration which is not possible from QMC like Active Directory setting,command center configuration,changing the database for creating QVPR(like from xml to sqlserver) etc
I hope you already have the idea about QMC and QEMC and the difference between them. Just wanted to sum it up and inform you how the difference has become irrelevant after the release of QlikView 11.
Server Handling Capability (prior to QV11 scenario)
QMC stands for QlikView Management Console.
QMC can handle only one instance of QV server and only one execution instance of QV publisher. So if you have a single server in your setup, QMC should handle it fine.
QEMC stands for QlikView Enterprise Management Console.
From a single QEMC, you can control multiple QV Server instance and multiple execution instances of QV publisher.
Tasks Achieved (prior to QV11 scenario)
If you have QVS only in your environment and no QVP, still the QMC will give you basic reload and scheduling capability. If QVP is installed, then along with basic scheduling option, you will have the usual QVP interface for doing other publisher tasks.
For using QEMC, you need to have QVP installed. In QEMC, you will have a full-fledged wizard to manage all settings and configuration tasks and services like command center configuration, AD settings, QVPR creation and management, managing of reload-distribute and other tasks (as ashoksenthil already mentioned).
Post QV11 Scenario
Why I said the diffrence is irrelevant now is, starting QlikView 11, QMC and QEMC are merged into a single unit, QlikView Management Console or QMC. Basically, QlikTech removed QMC and renamed QEMC as QMC.