There is a conversion process that is needed when migrating Visual Studio 2005 web site to Visual Studio 2008 web application projects.
It looks like VS2008 is creating a .designer. file for every aspx when you right click on a file or the project itself in Solution Explorer and select 'Convert to Web Application.'
What is the purpose of these designer files? And these won't exist on a release build of the web application, they are just intermediate files used during development, hopefully?
They hold all the form designer stuff that used to go in the #Region " Web Form Designer Generated Code " section of the code. instead of putting it in the .aspx.vb file where people might edit it (mistakenly or not), it's been moved to a separate file, so that you don't have ever look at it.
What kibbee said.
For the part of your question about existing on a release build, it depends on what kind of web site you have. If you have a pre-compiled web site, then none of code files (.vb, .cs, etc) need to be deployed the server. They are compiled into .dlls (assemblies) and deployed that way along with the .as*x files.