Gnome-Shell and Cinnamon behave differently, which includes how tray notification icons are being treated. While Cinnamon uses the classic approach of showing them, the Gnome-Shell developers would like to see them avoided.

Therefore it's currently the application's job to figure out what to do. Unfortunately Gnome-Shell and Cinnamon have many similar properties from an application's point of view, so it's necessary to find a way to distinguish them from within the code.

Thanks to Bastien Nocera and Shaun McCance for suggesting the use of D-Bus to distinguish between Gnome-Shell and Cinnamon.

As I was driven to fix the deja-dup backup tool, I was looking for a solution in the Vala programming language, and below is some code to detect a running Cinnamon desktop environment. I tested that the code works in Cinnamon version 1.4.0 and 1.6.7.

[DBus (name = "org.Cinnamon")]

public interface cinna : GLib.Object {
    public abstract string CinnamonVersion { owned get; }
}

int main (string[] args) {
    string cv;

    try {
	cinna c = GLib.Bus.get_proxy_sync (BusType.SESSION, "org.Cinnamon", "/org/Cinnamon");
	cv = c.CinnamonVersion;
    } catch (Error e) {
        stderr.printf ("%s\n", e.message);
        return 1;
    }

    if (cv == null) {
	stdout.printf ("not running cinnamon\n");
    }
    else {
	stdout.printf ("running cinnamon version %s\n", cv);
    }

    return 0;
}

I'd like to thank Evan Nemerson who helped me understand the correct syntax to access a D-Bus property using Vala.

Update March 18
Below is a reverse test, which tests for a property found in Gnome-Shell:

[DBus (name = "org.gnome.Shell")]
public interface GnomeShell : GLib.Object {
    public abstract string ShellVersion { owned get; }
}

int main (string[] args) {
    string gsv = null;

    try {
	GnomeShell gs = GLib.Bus.get_proxy_sync (BusType.SESSION, "org.gnome.Shell", "/org/gnome/Shell");
	gsv = gs.ShellVersion;
    } catch (Error e) {
        stderr.printf ("%s\n", e.message);
        return 1;
    }

    if (gsv == null) {
	stdout.printf ("not running gnome-shell\n");
    }
    else {
	stdout.printf ("running gnome-shell version %s\n", gsv);
    }

    return 0;
}