The command I'm using to start the Appium server:
node appium --address 127.0.0.1 --port 4723 --session-override --no-reset --platform-name Android --platform-version 23 --automation-name Appium
How would I stop the server through command line?
Ctrl+c
or
ps -A | grep appium
kill [process ID]
If you're looking to do this programmatically, see http://discuss.appium.io/t/launching-and-stopping-appium-server-programmtically/700.