I've just started working with Web applications in VS.NET 2003. One big gripe: I hate the mess with Virtual Directories scattering files all over the place.
Thank goodness I picked up a copy of Expert .NET Delivery Using NAnt and CruiseControl.NET by Marc Holmes. I found a gem of a reference tucked in all the other great info in the book: Swapping Web Projects for Class Libraries. None other than Fritz Onion has a Wiki site explaining the steps involved. He also gives a bit of background on why he does web apps this way.
Fritz's hack I mean trick gives you the web component wizards within class library projects.
Much cleaner, much simpler.