This article should do well in displaying the ability to use
Visual Studio 2005 and SharePoint 2007 to build and deploy Application pages
for your needs. Certainly not all circumstances are the same of course, and not
everything shown here may align perfectly with what you are looking to do, but
I certainly hope it does provide a good start point for not only beginning your
construction and use of Application pages, and deploying them, but also how to
make some simple changes to your menus for the purpose of accessing your custom
pages, whether they are Application pages or Site pages.