I just committed a rather nice piece of functionality to the FFmpeg Wrapper module. Files that are attached to Drupal nodes can be transcoded multiple times by a simple interface. Once you find settings that you like, you can attach your transcoded file back to the original node.
Whether you need to create a file for download, create a web-friendly format from a file, or just want to offer a high or low bandwidth versions, any file that is attached to a Drupal node via the upload form and can be transcoded with this tool.
FFmpeg Wrapper puts a link on the file attachments list to the FFmpeg Wrapper testing tool on files that FFmpeg can transcode- which helps identify bad file types quickly.