Are these projects located in different working copies, or is every project in the same WC?
They are all in the same working copy.
How can I create a web site project? I have VS 2008 standard, but don't see this type of project. Do I need to install an extension or did I miss something during installation? I'd like to reproduce the problem, makes it way easier to fix :)
You probably have to install the Visual Web Developer portion of VS 2008 standard to be able to create website projects. In Help/About dialog, under Installed products, I see:
Microsoft Silverlight Projects 2008
Microsoft Visual Basic 2008
Microsoft Visual C# 2008
Microsoft Visual Web Developer 2008
and then a bunch of updates, hotfixes, Service Pack 1, and extensions I have installed. If you're missing the fourth line, go back to Setup.