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I use Adobe Lightroom with a plugin (LRS/Mogrify) which works great, can't say enough good things about lightroom for photography. The plugin itself actually uses an application called ImageMagick.
I'm new, or I'd post a link for you, but a quick google of "imagemagick watermark" will give you a page showing you what it can do. It's lightweight and free and it'll probably do what you need. I think a lot of other programs use it as their image manipulation engine.
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