There probably has been billions of articles written about this topic, and I am no expert who understands the full extent on how the two types of project differ from each other. However, most of those articles are fairly old, and the year 2011 deserves a new article about this topic. :)
So if you are a developer working in a Microsoft shop, chances are you would use at least one of the following: ASP.NET MVC, NuGet, Unity Application Block, Unit Test, Gated Check-in, custom build event/script.
If you use any of those consistently in your projects, it's probably best to stick with Web Application Project, some of them (i.e. ASP.NET MVC) flat out cannot work with Website Project; some would, but requires non-typical setup which you have to investigate and assess.
Conclusion: in year 2011, if you are not sure, use Web Application Project.
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