I would like to find an application that I can use to convert any video format in .mpv4 or .ogg from the command line.
I don't mind it cost money as long it worth it.
Which one would you recommend?
I think you could take a lok to Avidemux, ti is multiplatform, support many formats (included mp4) and support command line interface. There is also a good scripting engine if you need more powerfull usage.