Did you ever wonder where those sites went if you create one under the Sites directory within SharePoint Portal Server? I did! If you try to list a sites by using the SPSite.AllWebs they will not show up. Why? So far as I can see they are created as "floating" sites. But there is a way to list them. The Sites directory is a Area and can be found easily.

First create a TopologyManager and retrieve the PortalSite object by using an Uri object.

TopologyManager topologyManager = new TopologyManager();
Uri uri = new Uri("http://localhost/");

PortalSiteCollection sites = topologyManager.PortalSites;

PortalSite portalSite = sites[uri];

Then get the PortalContext and use this to get the Guid of the SystemArea. The SystemArea is an enumeration providing you some starting points of Areas.

PortalContext portalContext = PortalApplication.GetContext(portalSite);

Guid homeGuid = AreaManager.GetSystemAreaGuid(portalContext, SystemArea.Home);

Based on the Guid its very easy to retrieve the actual Area object. And based on that Area object we retrieve the Sites Area object from its children.

Area homeArea = AreaManager.GetArea(portalContext, homeGuid); 
Area sitesArea = homeArea.Areas["Sites"];

Loop through the AreaListings in this Area object and check if its type is ListingType.Site. The URL property contains the url to the created sites.

foreach(AreaListing listing in sitesArea.Listings)
{
   if (listing.Type == ListingType.Site)
   {
      output.WriteLine(String.Format("{0} ({1})<br>", listing.Title, listing.URL));
   }
}