Sometimes is annoying having all this popups when VLC is minimized and track changes.
Here is how to disable them (for version 1.x):
Go to Tools-> Preferences -> All -> Interfaces -> Main Interfaces -> Qt
and uncheck Notify on track change.
And since interface changed in new version (For version 2.x)
Go to Tools-> Preferences -> Interface -> Show media change popup
and change to Never
Here is a screenshot for reference:
Added by request(Trevor):
If you want to remove systray icon just above there is the setting “Show Systray Icon”. Uncheck it to remove icon from systray.