WCF
The Silverlight Multi File Upload control was originally made using WCF webservies. Each file was uploaded in multiple small chunks. This results in a lot of small chuncks, and a lot of requests to the webserver.
HttpHandler
An alternative way of uploading is using a HttpHandler to receive the file in big chunks of 4MB. The result is less overhead and a faster upload experience.

The Silverlight Mulit File Uploader now supports uploading using a HttpHandler. The HttpHandler is included in the project (HttpUploadHandler.ashx). To use it, add the following initParameter: HttpUploader=true
Example usage is shown on this page in the project: HttpUploader_SilverlightMultiFileUploadTestPage.aspx)

PHP
Another advantage of the HttpHandler option is that it's easier to write a PHP version of the handler. The included HttpHandler is written in C#.

Example
Download changeset 8572 or later on CodePlex and see the included testpage (HttpUploader_SilverlightMultiFileUploadTestPage.aspx)

You can see the control in action here.