http://www.plupload.com - "Allows you to upload files using HTML5 Gears, Silverlight, Flash, BrowserPlus or normal forms, providing some unique features such as upload progress, image resizing and chunked uploads." This is the uploader used in current WordPress v3.4.1 and the best one out there in my opinion.
It comes with upload.php file (full file: http://ideone.com/xbPUS).
I have doubts about its security: When I have upload.php on my server and even if I don't setup any Javascript for Plupload anyone is still able to relatively easy send request to upload.php file and upload anything, anytime... TRUE OR FALSE?
How do I prevent that?