I have this ready. Just designed using PHP last week and used on 43000 different images of different sizes (all .jpg, .gif) distributed across 2700 folders and sub folders
You can design your own watermark as a .png with a suitable level of transparency in adobe photoshop or coreldraw in any size and tell the path of your watermark image to the script
Script will automatically resize the watermark image into the size of the original image and produce the watermarked image
Piece of mind, just choose your folders, sit back and relax, see this working
Its in PHP and I can configure it on your linux server
Thanks