- gMail-esque upload (.Net)
- SWF Upload (flash/js, but backend agnostic)
- MultiFile (jQuery, but backend agnostic)
- jUpload (java, but backend agnostic)
- File Chucker (PHP and Perl)
- …and my personal favorite, jQuery form plugin which handles all of your ajax and file uploads at once. Very nice, highly recommended as is jQuery.
Using Ajax in your website makes you buzzword compliant these days (OMG teh Web 2.0!?!), but once the hype passes I think everyone will agree then when used properly, it can greatly enhance the user experience.