With VS 2005 sp1 a web application project (which puts all webpages in a single assembly) is again a standard project type. What you have to watch yourself is the support in a deployment project. Having created a "web setup" project you see the folder tree on the target machine. This does include a bin folder.
It's up to you to include the right files in the right folders.
- Content files in the root.
- Primary project output and all loose referenced assemblies in the bin folder.
No big deal; but it's better to know this in advance instead of finding out behind your customers machine J