Example of markers in multiple layers with Leaflet markercluster. Copied from a project using Twitter Bootstrap and jQuery.

markercluster_multi-layer-markers.html

<div id="map-buttons" class="btn-group" data-toggle="buttons-checkbox">
  <button id="layer1" class="btn active">Layer 1</button>
  <button id="layer2" class="btn active">Layer 2</button>
  <button id="layer3" class="btn active">Layer 3</button>
</div>

<script type="text/javascript">
// Setup "layer" arrays
layer1Array  	= new Array();
layer2Array		= new Array();
layer3Array		= new Array();

layers_visible = ["layer1Array", "layer2Array", "layer3Array"];

var markers = new L.MarkerClusterGroup({ disableClusteringAtZoom: 17 });

	// Example of creating a marker and putting in a layer. These steps are repeated for all markers.

	var marker1 = new L.Marker(new L.LatLng(LAT_HERE, LONG_HERE)).bindPopup("You clicked on the marker.");

	// Put marker in appropriate layers
	layer1Array.push(marker1);
	layer3Array.push(marker1);

	// Get marker on the map
	markers.addLayer(marker1);

// Add all markers to map
map.addLayer(markers);

// Functions that make layering work
 
Array.prototype.contains = function(v) {
    for(var i = 0; i < this.length; i++) {
        if(this[i] === v) return true;
    }
    return false;
};

Array.prototype.unique = function() {
  var arr = [];
	for(var i = 0; i < this.length; i++) {
		if(!arr.contains(this[i])) {
			arr.push(this[i]);
		}
	}
	return arr;
}

refreshLayers = function() {
  	markers_visible = [];
		for(i = 0; i < layers_visible.length; i++) {
			markers_array = window[layers_visible[i]]; // select the array
			markers_visible = markers_visible.concat(markers_array);        // add contents to markers_visible
		}

		markers_visible = markers_visible.unique(); // remove duplications from array caused when marker is in multiple visible layers

		markers.clearLayers(); // remove all markers from map
		markers.addLayers(markers_visible); // add back markers currently visible
	}

$("div#map-buttons").delegate("button", "click", function() {
  layer_array = $(this).attr("id") + "Array";

	// update layers_visible array
	if($(this).hasClass("active")) { // Note: I was using Twitter Bootstrap, which toggles the "active" class, but this delegated click is triggered first
		// remove from array
		layers_visible.splice(layers_visible.indexOf(layer_array), 1);
	} else {
		// add to array
		layers_visible.push(layer_array);
	}

	refreshLayers();
});
</script>

Is there any working example on this? I'd be very happy to see it. Thanks!