I have the following requirements for a compression software application. I don't know if it is realistic, but these would be the ideal things.
1. Batch compression
2. Includes progressive download MP4 compression
3. Ability to add watermark when encoding
4. Ability to join two clips in encoding process (I need tack a disclaimer to the end of otherwise finished clips, and it can't be done prior to the encoding process due to other limitations and the need for efficiency in our work flow).
5. Needs to run on windows platform
Sorenson seems to do all of the above, except #4 (as far as I can tell). I haven't found one that can do all five yet.