If you have hundreds of pictures that you are wanting to watermark, this way is a little easier than doing it by hand, In Photoshop, all you have to do is:
1. make a seperate .psd with your transparent watermark in it.
2. make a stock folder where your watermark .psd is, and where your stock photos are to be watermarked.
3. make a new folder for the processed watermarked images to go.
4. create a new action in photoshop to carry out watermarking your images.
http://imagehost.vendio.com/preview/od/odb/action.jpg
5. when you hit record in here, you will need to do the first one manually to show photoshop what it is you want to automate.
6. after your action is finished recording, all you have to do is go to File > Automate > Batch and it will process the each individual image on the folder you chose, with the action that you created.
** I only tried this on all the same sized images. For different sizes i.e. Main, Thumbnail, you may need to create seperate actions.