Web apps are nice for users since they don't have to deal with deployment pains, but the developers still have to worry about it. Most developers I know are still manually deploying apps to servers by hand. Others are using the built-in deployment tools in Visual Studio 2010 or third-party deployment tools. Some folks write their own deployment systems. And other developers have application servers with built-in deployment capabilities.
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Justin James is the Lead Architect for Conigent.