There are many tools, including free ones that allow for video conversion, however, many of them use GUIs and don't allow for automation of tasks. FFmpeg is a command line based tools which allows to do very neat video manipulations.
We would like to share this small script, which our IT specialists have used for one of our video conversion projects. It parses a directory, finds all flv (Flash video) files and converts them to mp4. This script can be added to a cronjob to run on a scheduled basis. Converted videos can be moved elsewhere upon completion.
As mentioned, we've used ffmpeg to accomplish this task, running under Ubuntu 14.04. FFmpeg doesn't come with Ubuntu 14.04 and a package repository needs to be added manually first.