We do a lot of web applications that manage scientific data. Uploading files (data files, images, study documents) with just Javascript and HTML takes a lot of code, and the user doesn't get a good, simple multiple file selector.
You can use an ActiveX control such as the tools at http://www.aurigma.com/, but installing ActiveX can be difficult in some environments.
We decided to use Silverlight's capabilities, and the result is the Silverlight File Uploader project which we submitted as open source to CodePlex. The user experience is quite good, and it is easy to slot this component into your own web project.
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