This usually refers to an "app bundle ID". This is an ID for the file that will become your app on the store. You set this ID when you create your app.
Note there is also an "Apple app ID" which is the ID Apple gives to your "app project" in iTunes connect.
In all cases, except one, when we say App ID, we mean the former. The exception is when you are uploading your .ipa to iTunes Connect with the .ipa loader.