Formatted JS:

var map, bounds, geocoder, markers = [],
  pollies, pinImage, pinColor = '00FF00',
  defaultPinColor = 'F75850',
  defaultPin;
$('#controls input[name="[counties]"]').click(function() {
  var poly = pollies[this.value];
  if (poly.map) {
    poly.infowindow.close();
    poly.setMap(null);
    this.checked = false;
  } else {
    poly.setMap(map);
    this.checked = true;
  }
});

function elapsed(rfd) {
  var rs = (new Date().getTime() - rfd.getTime()) / 1000,
    days = Math.floor(rs / 86400),
    hours = Math.floor((rs - (days * 86400)) / 3600),
    minutes = Math.floor((rs - (days * 86400) - (hours * 3600)) / 60),
    secs = Math.floor((rs - (days * 86400) - (hours * 3600) - (minutes * 60))),
    fet = secs + 's';
  if (minutes) {
    fet = minutes + 'm' + ' ' + fet;
  }
  if (hours) {
    fet = hours + 'h' + ' ' + fet;
  }
  if (days) {
    fet = days + ' Day' + (days > 1 ? 's' : '') + ' ' + fet;
  }
  return 'Created: ' + rfd.toLocaleTimeString().toLowerCase() + ',<br>' + fet + ' ago';
}

function createMarker(latlng, html, map) {
  var ref = $.trim($('#reference').val()),
    infowindow = new google.maps.InfoWindow({
      content: ref || html
    }),
    marker = new google.maps.Marker({
      map: map,
      time: new Date(),
      position: latlng,
      html: html,
      icon: defaultPin,
      infowindow: infowindow
    }),
    $tm = $('#themarkers').append('<option value="' + html + '" title="' + infowindow.content + '">' + html + '</option>');
  $tm.get(0).selectedIndex = 0;
  marker.addListener('mouseover', function() {
    clearInterval(infowindow.timer);
    infowindow.setContent((ref || html) + '<br>' + elapsed(marker.time));
    $('#supplementwindow').html(infowindow.content).fadeIn();
    infowindow.timer = setInterval(function() {
      infowindow.setContent((ref || html) + '<br>' + elapsed(marker.time));
      $('#supplementwindow').html(infowindow.content);
    }, 300);
    infowindow.open(map, this);
  });
  marker.addListener('mouseout', function() {
    clearInterval(infowindow.timer);
    infowindow.close();
    $('#supplementwindow').fadeOut();
  });
  marker.addListener('click', function() {
    var oe = this.optel;
    $tm.get(0).selectedIndex = $('option', $tm).index(oe);
    $tm.trigger('change');
  });
  marker.optel = $('option', $tm).last();
  $tm.get(0).size = $('option', $tm).length;
  markers.push(marker);
}
$('#formcont form').submit(function(e) {
  var addresses = $('.address', this);
  addresses = [addresses.eq(0).val(), addresses.eq(1).val()];
  addresses.forEach(function(address, refnum) {
    if (address) {
      geocoder.geocode({
        'address': address
      }, function(results, status) {
        if (status == google.maps.GeocoderStatus.OK) {
          map.setCenter(results[0].geometry.location);
          createMarker(results[0].geometry.location, address, map, refnum);
          bounds.extend(results[0].geometry.location);
          map.fitBounds(bounds);
        } else {
          alert("Geocode was not successful for the following reason: " + status);
        }
      });
    }
  });
  e.preventDefault();
});
$('#activatemarker').click(function() {
  var tm = $('#themarkers'),
    si = tm.get(0).options.selectedIndex,
    $o = $('option', tm).eq(si),
    i = $o.val();
  if (!i) {
    return;
  }
  $.each(markers, function(idx, v) {
    if (v.html === i) {
      v.setIcon(pinImage);
      return false;
    }
  });
});
$('#removemarker').click(function() {
  var tm = $('#themarkers'),
    si = tm.get(0).options.selectedIndex,
    $o = $('option', tm).eq(si),
    i = $o.val();
  if (!i) {
    return;
  }
  $.each(markers, function(idx, v) {
    if (v.html === i) {
      v.setMap(null);
      markers.splice(idx, 1);
      return false;
    }
  });
  $o.remove();
  bounds = new google.maps.LatLngBounds();
  if (markers.length) {
    $.each(markers, function(i, v) {
      bounds.extend(v.position);
    });
    map.fitBounds(bounds);
  }
  if (markers.length < 2) {
    map.setZoom(markers.length ? 13 : 8);
  }
  tm.get(0).size = $('option', tm).length;
});
$('#themarkers').change(function() {
  this.title = this.options[this.options.selectedIndex].title;
  var i = this.value;
  if (!i) {
    return;
  }
  $.each(markers, function(idx, v) {
    if (v.html === i) {
      map.setCenter(v.position);
      map.setZoom(10);
      return false;
    }
  });
  this.size = $('option', $(this)).length;
});
$('#showall').click(function() {
  $('#themarkers').get(0).selectedIndex = 0;
  if (!markers.length) {
    map.setCenter(new google.maps.LatLng(52.178227, -0.46013));
    map.setZoom(8);
    return;
  }
  map.fitBounds(bounds);
  if (markers.length === 1) {
    map.setZoom(8);
  }
});

function formatCodes(codeString) {
  var a = codeString.split(' '),
    l = a.length,
    po;
  while (--l > -1) {
    po = a[l].split(',');
    a[l] = {
      lat: +po[1],
      lng: +po[0]
    };
  }
  return a;
}

function initMap() {
  pinImage = new google.maps.MarkerImage("http://chart.apis.google.com/chart?chst=d_map_pin_letter&chld=%E2%80%A2|" + pinColor);
  defaultPin = new google.maps.MarkerImage("http://chart.apis.google.com/chart?chst=d_map_pin_letter&chld=%E2%80%A2|" + defaultPinColor);
  var p;
  geocoder = new google.maps.Geocoder();
  bounds = new google.maps.LatLngBounds();
  map = new google.maps.Map(document.getElementById('map'), {
    zoom: 8,
    center: {
      lat: 52.178227,
      lng: -0.4013
    },
    mapTypeId: google.maps.MapTypeId.ROADMAP
  });
  pollies = {
    Bedfordshire: {
      paths: BedfordshireCodes,
      strokeColor: '#FF0000',
      strokeOpacity: 0.8,
      strokeWeight: 2,
      fillColor: '#FF0000',
      fillOpacity: 0.15,
      latlng: {
        lat: 52.002974,
        lng: -0.465139
      }
    },
    Bedford: {
      paths: BedfordCodes,
      strokeColor: '#FFC0CB',
      strokeOpacity: 0.8,
      strokeWeight: 2,
      fillColor: '#FFC0CB',
      fillOpacity: 0.15,
      latlng: {
        lat: 52.135973,
        lng: -0.466655
      }
    },
    Hertfordshire: {
      paths: HertfordshireCodes,
      strokeColor: '#FFFF55',
      strokeOpacity: 0.9,
      strokeWeight: 2,
      fillColor: '#FFFF55',
      fillOpacity: 0.25,
      latlng: {
        lat: 51.809782,
        lng: -0.237674
      }
    },
    Cambridgeshire: {
      paths: CambridgeshireCodes,
      strokeColor: '#00FF00',
      strokeOpacity: 0.8,
      strokeWeight: 2,
      fillColor: '#00FF00',
      fillOpacity: 0.15,
      latlng: {
        lat: 52.305297,
        lng: 0.021820
      }
    },
    Northamptonshire: {
      paths: NorthamptonshireCodes,
      strokeColor: '#0000FF',
      strokeOpacity: 0.8,
      strokeWeight: 2,
      fillColor: '#0000FF',
      fillOpacity: 0.15,
      latlng: {
        lat: 52.272994,
        lng: -0.875552
      }
    }
  };
  for (p in pollies) {
    var polly = pollies[p];
    polly.paths = formatCodes(polly.paths);
    polly = pollies[p] = new google.maps.Polygon(polly);
    polly.infowindow = new google.maps.InfoWindow({
      content: p,
      position: polly.latlng
    });
    polly.addListener('click', function() {
      if (this.infowindow.map) {
        this.infowindow.close();
      } else {
        this.infowindow.open(map, this);
      }
    });
    polly.setMap(map);
  }
}

function initialize() {}
google.maps.event.addDomListener(window, 'load', initialize);