I always use the "Publish Web Site" option to deploy my ASP.NET 2.0 projects. I do this for several reasons: I like knowing that the code in a production environment is the same as the code in my development environment, I know that published (compiled) pages exhibit better performance than uncompiled pages, and I like that the source code of my web applications need not be deployed along with the application itself.

However, "Publish Web Site" deployment has its own bugaboos. There are three files for each published web page that must be kept in sync, and for large web sites there are often hundreds of files in the BIN directory. Updating the code for just a single directory or page can be daunting.

The VB2005 Web Deployment Project addresses this issue. Using this free Microsoft add-in, web applications can be compiled either to a single dll or (as I prefer) to one dll per directory. This makes deployment of site updates much easier.

More information about the VB2005 Web Deployment Project is available on Scott Gunthrie's blog, here:
http://weblogs.asp.net/scottgu/archive/2005/11/06/429723.aspx