I am looking for a program that will compress/encode multiple MPEG files at one time?

You may compress all the files located under a folder in your computer. Under a windows operating system, simply right click the folder and select properties. From there, click a on labeled "Advanced" where you will find an option to compress files to save disk space. Then click apply to the set option. You will be prompted with an option to apply the setting to all contents and sub-folders inside. Select this option and click ok and you are set.