HandBrake is an open-source, GPL-licensed, multiplatform, multithreaded video transcoder, available for macOS X, Linux, and Windows which comes with its own GUI for converting videos, etc. Joseph has developed an Air Based app, DropFolders which can help you automate your video conversion using handbrake libraries in the back.
So as a summary, if you have a lot of videos that get processed in the more or less the same way every day, DropFolders can watch all of them every second and convert them to the format you want using the handbrake library the minute they arrive in a folder that is being watched.
You can create as many presets or rules you want and each rule will have its own pair of folders they watch. Also, you get a complete error log if anything goes wrong.
AIR 2.0 “DropFolders” Walkthrough from Joseph Labrecque