<t>Website:<br/>
<br/>
The Web Site project is compiled on the fly. You end up with a lot more DLL files, which can be a pain. It also gives problems when you have pages or controls in one directory that need to reference pages and controls in another directory since the other directory may not be compiled into the code yet. Another problem can be in publishing.<br/>
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If Visual Studio isn't told to re-use the same names constantly, it will come up with new names for the DLL files generated by pages all the time. That can lead to having several close copies of DLL files containing the same class name,<br/>
which will generate plenty of errors. The Web Site project was introduced with Visual Studio 2005, but it has turned out not to be popular.<br/>
<br/>
Web Application:<br/>
<br/>
The Web Application Project was created as an add-in and now exists as part<br/>
of SP 1 for Visual Studio 2005. The main differences are the Web Application Project<br/>
was designed to work similarly to the Web projects that shipped with Visual Studio 2003. It will compile the application into a single DLL file at build<br/>
time. To update the project, it must be recompiled and the DLL file<br/>
published for changes to occur.<br/>
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Another nice feature of the Web Application<br/>
project is it's much easier to exclude files from the project view. In the<br/>
Web Site project, each file that you exclude is renamed with an excluded<br/>
keyword in the filename. In the Web Application Project, the project just<br/>
keeps track of which files to include/exclude from the project view without<br/>
renaming them, making things much tidier.<br/>
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Reference<br/>
<br/>
The article ASP.NET 2.0 - Web Site vs Web Application project also gives reasons on why to use one and not the other. Here is an excerpt of it:<br/>
<br/>
- You need to migrate large Visual Studio .NET 2003 ap<br/>
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