imagemagick
http://www.imagemagick.org/script/index.php
its a server side program you can use to resize or otherwise manipulate images. I have a plugin on my company website setup to resize my uploaded images in 3 sizes, and add a watermark to the largest size when i upload a new product (i didn't program the thing, i'm not that smart, but i did configure it to use a png file of my watermark it would then merge with my files on upload.)
to do your whole site, you'd probably have to setup some kind of custom script to feed the converted files into a new directory using identical filenames, check them, and then copy them to the old directory.