I've been searching a long time for such a software. What I need to do is this: I have a million (figuratively) flv files that I need to convert to all mobile video formats (mp4,3gp etc with different codec/resolution/specs). I have to convert a gazillion files and what I need is a tool that can convert each file to all my needed formats by batch. My idea is the program must have a one-time profile setting (where I can set all the needed formats and their specs) that I will use for all conversions. Setting formats for each file is very time consuming. Please suggest apps and I will research them as this task is very crucial to me.
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ffmepg: you can do everything by command line, so you can batch it up.
There are a number of guis that you can use to help get the command line syntax right: it's rather complex.
For example, gui4ffmpeg.