Hi, > My suspicion is that guake does not use X11 embed anymore (which is > the API provided by the notification area applet), but the Indicators > API. > > Try installing and adding mate-indicator-applet and check if you find > guake's icon in there.
It's not going to work in Debian... mate-indicator-applet is just a container, it needs indicator-* packages to display the actual content. It's better to try this in Ubuntu. It has indicator-application, indicator-sound and other similar packages.