The "Sites" area has a list with links to Wss Toplevel sites.
This list is only updated when you create Wss from this "Sites" area.
But you can get hold on the list this way.
Area sitesArea = AreaManager.GetSystemAreaGuid(
Microsoft.SharePoint.Portal.PortalContext.Current,
Microsoft.SharePoint.Portal.SiteData.SystemArea.SiteRegistry);
SPList sitesList = sitesArea.web.Lists["sites"];
If you want to add your Wss Toplevel site to the index server, use the
SuggestDeepCrawl method.
And if you dont have the PortalContext.Current avialable then use the
TopologyManager class to get hold on the PortalSite and then get a
PortalContext from that.