Updated (2012.10.31):
I've removed this article due to this.
FlashUpload flash control to manage user uploads. It is a very powerful flash control that can let you customize the control. The price is affordabile (or you can try it free without limitations), and their customer service is outstanding. I use google talk to chat with them when I encounter any problem (also request some features!) with no problem.
OK, no more advertisement. :) Below is an example of what I've done for customizing it. The reason I put a blog here is because their document is good but not organized very well. I spent lots of time on puting things together... You can select many ways to integrate the flash control into your web app. Here I choose javascript.