You can either add markers one by one by calculating a location and adding the marker, or in the Flash API you can use an overlay. There is a very handy GeoRSS overlay that you just feed a Geocoded RSS file to. Each entry needs to have this:

GeoRSS Sample Item
<item>
  <title>M 3.3, Southern California</title>
  <description>November 08, 2005 22:03:46 GMT</description>
  <link>http://earthquake.usgs.gov/recenteqsww/Quakes/ci14197132.htm</link>
  <geo:lat>33.5325</geo:lat>
  <geo:long>-116.6910</geo:long>
  <dc:subject>3</dc:subject>
  <dc:subject>pasthour</dc:subject>
  <dc:subject>11.60 km</dc:subject>
</item>
Adding GeoRSS to the Flash map
<script type="text/javascript" 
       src="http://api.maps.yahoo.com/v3.0/fl/javascript/apiloader.js">
</script>
<div id="mapContainer" style="height: 500px; width: 930px;"></div>
<script type="text/javascript">
var mymap = new Map("mapContainer", "rlerdorf", "San Francisco, CA", 12);
mymap.addTool(new PanTool(), true);
mymap.addWidget(new NavigatorWidget()); 

olay = new GeoRSSOverlay('http://earthquake.usgs.gov/eqcenter/recenteqsww/catalogs/eqs7day-M2.5.xml');
mymap.addOverlay(olay);

</script>
Output
Ok, again, disappointing that we didn't need PHP. But to do the same on the DHTML map we need some PHP help. Although there is actually a DHTML GeoRSS overlay now.

Simple Embedded DHTML map
<script type="text/javascript" 
      src="http://api.maps.yahoo.com/ajaxymap?v=3.8&appid=rlerdorf">
</script>
<div id="jsmapContainer" style="height: 500px; width: 930px;"></div>
<?php
include 'simple_rss.php';
$url = 'http://earthquake.usgs.gov/eqcenter/recenteqsww/catalogs/eqs7day-M2.5.xml';
$feed = rss_request($url, $timeout=3600);
?>
<script type="text/javascript">
var marker = new Array();
var jsmap = new YMap(document.getElementById('jsmapContainer'));
jsmap.addPanControl();
jsmap.addZoomLong();
jsmap.drawZoomAndCenter("94089", 12);
<?php 
$i = 0;
while(!empty($feed[$i])) {
  $info = $feed[$i]['title'][0]."<br />";
  $mag = str_replace('.','',substr($info,2,3));
  $info .= $feed[$i]['description'][0]."<br />";
  $info .= '<a href="'.$feed[$i]['link'][0].'">more info</a>';
  $info = addslashes($info); 
  $lat = $feed[$i]['lat'][0];
  $lon = $feed[$i]['long'][0];
  echo <<<EOB
  marker[$i] = new YMarker(new YGeoPoint($lat,$lon)); 
  marker[$i].addLabel("$mag"); 
  YEvent.Capture(marker[$i], 
                 EventsList.MouseClick, 
                 new Function("marker[$i].openSmartWindow('$info');")); 
  jsmap.addOverlay(marker[$i]);
EOB;
  flush();
  $i++;
  if($i>99) break;
}
?>
</script>
Output