One issue has been that skype doesn't leave any way to bring itself back up if you click the "x" after launching it. It should leave an icon in the system tray but doesn't.
So I found a script that when relaunching skype instead of starting a second instance simply raises the existing instance. Simply replace the regular skype launcher with this.
#!/usr/bin/env python
import dbus
import sys
import os
try:
# Try and set skype window to normal
remote_bus = dbus.SessionBus()
out_connection = remote_bus.get_object('com.Skype.API', '/com/Skype')
out_connection.Invoke('NAME single-instance')
out_connection.Invoke('PROTOCOL 5')
#out_connection.Invoke('SET WINDOWSTATE MAXIMIZED')
out_connection.Invoke('SET WINDOWSTATE NORMAL')
out_connection.Invoke('FOCUS')
except:
os.system("skype")
sys.exit()
