Windows SharePoint Services 3.0 uses the following folder to deliver SharePoint administration pages to each site in the site collection:
%ProgramFiles%\Common Files\Microsoft Shared\Web server extensions\12\Template\Layouts
The layouts folder is a special directory that gets "virtualized" for each SharePoint site. That is, each SharePoint site will have a /_layouts path from the root of the Web. For example http://servername/sites/sitename/_layouts. You can make an ASP.NET 2.0 Web application available under each SharePoint site by deploying the application to the layouts folder. This How To illustrates deploying ASP.NET Web applications in the Windows SharePoint Services 3.0 _layouts folder.