In Lightroom 3 you can use the export dialogue. There is one box where you can choose a watermark or choose the option to create a new one. The watermark can simply be written in Lightroom or be any prepared image. Size, transparency, position etc. can be defined also. All adjustment are saved as a preset and will be used for all exports as long as you choose or create another one.
It's written for photoshop, but I found it worked pretty well in Gimp too.