I need to convert a 100s of video files from one format to another(to make them smaller) and insert our company's logo at the same time in all of them. I know how to batch convert video files but couldn't find how to insert logo in all of them at the same time. I don't want to insert logo one by one, which will be too time consuming. Can anyone recommend a good program for that?

You can (batch)convert the videofiles and insert a logo with Canopus Procoder 2.

Use the Help of Procoder and surch for logo. It is a video-filter called Bitmap keying filter.

I have never done it so I can't help you with it.