I'd recommend using WAP for any serious work. WAP provides standard Visual Studio project behaviors for all aspects of development while stock projects provide an easier getting going experience although as a project gets more complex it becomes a big hurdle IMHO.
The biggest issue with stock projects is that while it's easy to use, it's very complex behind the scenes - ASP.NET has to do all kinds of black magic with special tools to make this work as seamless as it appears. You can think of stock projects as a WYSIWYG project - it takes all your files and it just works as is. ASP.NET automatically handles compilation and fixups etc. However, if you plan on precompiling your site or not distributing your source code to the site it gets very hairy for any non-trivial projects. The good things about stock projects are:
No compilation required - it just works
Debugging: You can make a change and go right on debugging without restarting the debugger.
ASP.NET COmpiler can give you information about ASPX page code - better compile time error detection.
WAP is like VS 2003 where every CS or VB file must be compiled explicitly in VS.NET. All code behind files are compiled into a single assembly and you have to deploy both the ASPX files and the compiled assembly. Although it appears like this approach is more rigid with the explicit compile step it is more predictable and IMHO logical of how everything hangs together. It's also much easier to deploy a WAP project because you don't have an extra pre-compilation step as required with stock projects.
Finally WAP works properly with source control where stock projects did not (well sort of but there were serious issues).
I would use WAP for all 'real' work. I use stock projects for samples or demos or anything that's quick and dirty to check things out. It can be easier to work with stock projects when you just need to check something out quickly.
+++ Rick ---
>In VS 2005, I have an option for creating a new web site, and I have an option for creating a new web application. What is the difference, and which should be I be doing?
