Well, here's a way you can try.
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.
Some limitations of doing it this way is,
- can't seem to record the repositioning, so the watermark will be pasted to the middle of the image.
- the watermark will always be the same size, will not resize it self for larger or smaller images.
- you have to have the watermark copied to the clipboard before automating.
There are probably better ways, play around with the record action feature and Im sure you'll get it to do what you need.