How to stop a program running under Eclipse?
Those who find it tedious switching between perspectives to stop the program (like I did), you can view the devices windows in your current perspective by selecting
Windows > Show View > Other... > Android > Devices
I understand you want to stop your app on the emulator. For this you can open up the devices window (in the debug perspective), select the process and then press the stop button on the same window.
Keep in mind that on Android, programs generally only 'stop' if you finish() or the system destroys them when memory is required. Why stop at all? You do not need to stop to fix/re-install/re-test, for example.