here's a way you can try in PS.
1. Make yourself a watermark image, I created one on one layer that was semi transparent.
2. Copy the image so it is in your clip board (Ctrl - C).
3. Open up the actions pallette (alt-F9 in Windows).
4. Click new action (looks like the new layer button), name it whatever and hit record.
5. Open up a file you would like to add the watermark to and paste the watermark into it (Ctrl - V), position, change transparency, do whatever.
6. Merge the layers (if you don't you will have to save as psd)
7. Click stop on the actions pallette.
Now you have an action that will paste, set the transparency and merge the watermark on the image of your choosing.
To apply this to a folder of images go to "File" -" Automate" - "Batch". Select the action you just made, choose the source folder and click ok and sit back and watch Photoshop do your work for you.
You can also try Picture Watermarker for photo protection. It's quite easy to use. You can free download it on
http://www.sharewarecheap.com/Picture-Watermarker_software_1349.html