I\'m using ffmpeg to watermark videos with a PNG file using vfilters like so:
ffmpeg -i 26.wmv -vcodec libx264 -acodec copy -vf \"movie=logo.png [watermark];
Here is a set of very good examples http://ffmpeg.org/ffmpeg.html#Examples
Here is a script i made for converting files to flv video and also adding a preview image