I implemented it using Element.implement, but my question is asking for a native MooTools way to do it, without defining my own functions.
Element.implement({
    // Call as element.bind('event.namespace', function() {});
    bind: function(name, funktion) {
        // Get event type and namespace
        var split = name.split('.'),
            eventName = split[0],
            namespace = split[1];
        // Store the event by its full name including namespace
        this.bindCache = this.bindCache || {};
        if(this.bindCache[name]) {
            this.bindCache[name].push(funktion);
        } else {
            this.bindCache[name] = [funktion];
        }
        // Bind the function to the event
        this.addEvent(eventName, funktion);
    },
    // Call as element.unbind('event.namespace');
    unbind: function(name) {
        // Unbind the specified event
        var eventName = name.split('.')[0],
            funktions = this.bindCache[name],
            x = 0,
            funktion;
        for(; funktion = funktions[x++]; ) {
            this.removeEvent(eventName, funktion);
        }
    }
});
document.body.bind('click.1', function() {alert('click 1');});
document.body.bind('click.1', function() {alert('click 1 other');});
document.body.bind('click.2', function() {alert('click 2');});
document.body.unbind('click.1'); // leaves click.2