While there isn't any Solution Package items to add httpHandlers and other web.config edits, you can do these through Feature Receivers. Tony pointed this out in his post @ sharepointsolutions.blogspot.com, so I decided to update the code for the Atlas RC and add it to a Feature Reciever in the SharePoint.Ajax Codeplex Project. Otherwise, I've got this great installer technology that scales well across farms and enables no-touch dpeloyment EXCEPT for that httpHandler. That's really a bummer-- so I'm glad to have found a solution! We now have a complete no-touch deployment solution in place for the SharePoint Ajax components, which isn't bad for such a "young" project this early in development!

The Feature Reciever is defined in the Feature manifest with the following attributes:

ReceiverAssembly="SharePoint.Ajax, Version=1.0.0.0, Culture=neutral, PublicKeyToken=5ed42c8fcfe5cf7c"
ReceiverClass="SharePoint.Ajax.Config.FeatureReceiver"

This seems to work well in the Solution Package when the Feature is set to the SPWeb's scope, when handling the FeatureActivated method. It is now standard part of my Ajax project's Solution Package projects, including SharePoint.Ajax on Codeplex.  If you'd like to see the full source code, it's in change set 15970 or newer.

public const string ScriptResource = 
	@"<add verb=""GET,HEAD"" path=""ScriptResource.axd"" 
	type=""System.Web.Handlers.ScriptResourceHandler, System.Web.Extensions, Version=1.0.61025.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35"" 
	validate=""false"" />";

    public override void FeatureActivated(SPFeatureReceiverProperties properties) {
      SPWebApplication app = null;
      SPSiteCollection site = properties.Feature.Parent as SPSiteCollection;
      if (site == null) {
        SPWeb web = properties.Feature.Parent as SPWeb;
        if (web != null)
          app = web.Site.WebApplication;
      } else
        app = site.WebApplication;
      bool removeModification = false;

      if (app != null)
        AddAjaxHandlerToWebConfig(app, removeModification);
      else
        throw new ApplicationException("Could not locate a web application");
    }
    public static void AddAjaxHandlerToWebConfig(SPWebApplication app, bool removeModification) {

      SPWebConfigModification modification = new SPWebConfigModification(
        "add[@path='ScriptResource.axd']", "configuration/system.web/httpHandlers");
      modification.Owner = "SharePoint.Ajax";
      modification.Sequence = 0;
      modification.Type = SPWebConfigModification.SPWebConfigModificationType.EnsureChildNode;
      modification.Value = ScriptResource;

      if (removeModification)
        app.WebConfigModifications.Remove(modification);
      else
        app.WebConfigModifications.Add(modification);
      SPFarm.Local.Services.GetValue().ApplyWebConfigModifications();
    }

Again, thanks to Tony for the original post.

*Note: typo in AddAjaxHAndlerToWebConfig fixed on 1/10. Original post on 1/9.