Yesterday I replaced a Flex2 uploader I created (that just wasn't working properly in IE) with SWFUpload and found it to be a joy to work with. I looked all over (even at some jQuery plugins), but nothing I found was exactly what I needed (progress bar, multiple files, extendable with javascript). I don't think there is anything available out there to tie it together with jQuery, but just figured I throw it out there cause it appears to be the best solution for anyone looking to do a javascript based uploader. =)
Main site - http://swfupload.mammon.se/ Demo - http://swfupload.praxion.co.za/ Check out the application uploader demo for some very cool ways to use it.