So I found this article, http://weblogs.asp.net/soever/archive/2006/11/14/SharePoint-2007_3A00_-using-the-masterpage-from-your-site-in-custom-_5F00_layouts-pages.aspx, which explains how to use your SharePoint site's master page when you create a custom application page in the _layouts virtual directory. At this point in time I don't really have any custom application pages yet but I liked the idea of when I theme a site that all pages, including application pages in the _layouts virtual directory, use the same master page. By default all application pages use the application.master master page. After finding this article, http://www.odetocode.com/Articles/450.aspx, and a lot of playing around I believe I have found a solution. I created a HttpModule that on a page's preinit, it checks to see if the page is in the _layouts virtual directory, and if so, it will assign it the master page url from the current sharepoint site. Here's my code:

using System;
using System.Collections.Generic;
using System.Text;
using System.Web;
using System.Web.UI;
using System.Web.UI.WebControls;
using System.Configuration;
using System.Data.SqlClient;
using System.Data;
using Microsoft.SharePoint;

public class ApplicationMasterPage : IHttpModule
{
	public void Init(HttpApplication context)
	{
		context.PreRequestHandlerExecute += new EventHandler(context_PreRequestHandlerExecute);
	}

	void context_PreRequestHandlerExecute(object sender, EventArgs e)
	{
		Page page = HttpContext.Current.CurrentHandler as Page;
		if (page != null)
		{
			page.PreInit += new EventHandler(page_PreInit);
		}
	}

	void page_PreInit(object sender, EventArgs e)
	{
		Page page = sender as Page;
		if (page == null) return;
		if (page.MasterPageFile == null) return;
		HttpContext context = HttpContext.Current;
		string currUrl = context.Request.Url.ToString();
		string basepath = currUrl.Substring(0, currUrl.IndexOf(context.Request.Url.Host) + context.Request.Url.Host.Length);
		//Use RawUrl, otherwise it will always use the root web.
		currUrl = context.Request.RawUrl;
		if (currUrl.ToLower().Contains("/_layouts/") &&
			page.MasterPageFile.ToLower().EndsWith("application.master"))
		{
			currUrl = currUrl.Substring(0, currUrl.ToLower().IndexOf("/_layouts/"));
			SPSite site = null;
			SPWeb web = null;
            try
            {
				site = new SPSite(basepath + currUrl);
				web = site.OpenWeb(currUrl);

				if (String.IsNullOrEmpty(web.MasterUrl) == false)
	            {
					page.MasterPageFile = web.MasterUrl; 
					page.Load += new EventHandler(page_Load);
				}
			}
            finally
            {
                if (web != null)
                {
                    web.Dispose();
                }
                if (site != null)
                {
                    site.Dispose();
                }
            }
		}
	}

	public void Dispose()
	{
	}

	void page_Load(object sender, EventArgs e)
	{
		Page page = sender as Page;
		if (page == null) return;

		try
		{
			ContentPlaceHolder placeHolderTitleBreadcrumb = page.Master.FindControl("PlaceHolderTitleBreadcrumb") as ContentPlaceHolder;
			SiteMapPath contentMap = placeHolderTitleBreadcrumb.FindControl("ContentMap") as SiteMapPath;
			contentMap.CssClass = "ms-hidden";
		}
		catch { }

		try
		{
			ContentPlaceHolder placeHolderSearchArea = page.Master.FindControl("PlaceHolderSearchArea") as ContentPlaceHolder;
			placeHolderSearchArea.Visible = false;
		}
		catch { }
	}

}

Be sure to register the HttpModule in the web.config of your sharepoint site.

This did require me to add extra contentplaceholders into my default.master. Here are the two extra placeholders I had to add:

PlaceHolderPageDescriptionRowAttr
PlaceHolderPageDescriptionRowAttr2

To add these placeholders into my default.master I replaced the following code:

<PlaceHolder id="MSO_ContentDiv" runat="server">
<table id="MSO_ContentTable" width=100% height="100%" border="0" cellspacing="0" cellpadding="0" class="ms-propertysheet">
<tr>
<td class='ms-bodyareaframe' valign="top" height="100%">
<A name="mainContent"></A>
<asp:ContentPlaceHolder id="PlaceHolderPageDescription" runat="server"/>
<asp:ContentPlaceHolder id="PlaceHolderMain" runat="server">
</asp:ContentPlaceHolder>
</td>
</tr>
</table>
</PlaceHolder>

<PlaceHolder id="MSO_ContentDiv" runat="server">
<table id="MSO_ContentTable" width=100% height="100%" border="0" cellspacing="0" cellpadding="0" class="ms-propertysheet">
<TR valign="top" <asp:ContentPlaceHolder id="PlaceHolderPageDescriptionRowAttr" runat="server"/> >
<TD class="ms-descriptiontext" width="100%">
<asp:ContentPlaceHolder id="PlaceHolderPageDescription" runat="server"/>
</TD>
</TR>
<TR <asp:ContentPlaceHolder id="PlaceHolderPageDescriptionRowAttr2" runat="server"/>>
<TD ID=onetidMainBodyPadding height="8px"><IMG SRC="/_layouts/images/blank.gif" width=1 height=8 alt=""></TD>
</TR>
<tr>
<td class='ms-bodyareaframe' valign="top" height="100%">
<A name="mainContent"></A>
<asp:ContentPlaceHolder id="PlaceHolderMain" runat="server">
</asp:ContentPlaceHolder>
</td>
</tr>
</table>
</PlaceHolder>

I also had to change my default breadcrumbs code in the default.master to match the application.master. I replaced the following code:

<asp:contentplaceholder id="PlaceHolderTitleBreadcrumb" runat="server">
	<asp:sitemappath id="ContentMap" runat="server" sitemapprovider="SPContentMapProvider" skiplinktext="" nodestyle-cssclass="ms-sitemapdirectional"></asp:sitemappath>  
</asp:contentplaceholder>

with

<asp:contentplaceholder id="PlaceHolderTitleBreadcrumb" runat="server">
	<asp:SiteMapPath SiteMapProvider="SPXmlContentMapProvider" SkipLinkText="" NodeStyle-CssClass="ms-sitemapdirectional" runat="server"/>
		 
	<asp:SiteMapPath SiteMapProvider="SPContentMapProvider" id="ContentMap" SkipLinkText="" NodeStyle-CssClass="ms-sitemapdirectional" runat="server"/>
</asp:contentplaceholder>

--------------------------------------------------------------------------------------------------

Update (02/23/08): I've changed my default.master and my httpmodule around a lot since posting this. If you don't compile a dll you will need to place the ApplicationMasterPage.cs file in a App_Code directory of your root site and in a App_Code directory at C:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\12\TEMPLATE\IMAGES. You can download my latest files below:

default.master

ApplicationMasterPage.cs

--------------------------------------------------------------------------------------------------

All of the code and changes ended up with a site settings page that looks like this.

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