Is there a great uploader script that uses jQuery, like uploadify, but with a fallback option for when flash is not available?
I tried FancyUpload, which has this and uses an invisible IFRAME to do its stuff. The problem is, it's built on top of Mootools (conflicts everywhere because I can't change my whole codebase to use jQuery instead of $ if I use jQuery.noConflict(), and I really don't think it's a good idea to mix js libraries like that).
http://www.plupload.com/ falls back from HTML5 to Flash, Gears, Silverlight and iFrame. It's developed for TinyMCE, so it's extensively tested and actively developed. One downside could be the size, but simply include it only on the sites that need to upload files and reduce size but excluding Gear or Silverlight support.
I am the author of FancyUpload, so believe me when I approve another uploader ;)
Sebastian Tschan just released a great plugin called jQuery File Upload that will likely suit your needs.