I'm amazed that this app hasn't been updated since 2011 and still beats its competitors in some points!
I've tested quite everything available on the market, free and paid ones, there are surely a lot of apps that can do precisely complex conversions with the exact settings you want, but I was searching for a simple and fast way to set down the resolutions of films to watch them on my Dell Mini 9 (which is not the state of the art of modern computing, but very handy with its small size ;-) ): normally sized films are usually played with a lot of stuttering, so I choose the "iPod/iPhone" setting on Media Converter, the file gets bigger (a 850 Mb film becomes 1.3 Gb) but it's played fluently on my DM9!
Note that the conversion is done with ffmpeg at 64 bits (check it in Activity Monitor).
I've just tried to substitute the ffmpeg file inside the package with the latest available but it crashes, so I'll stick with Media Converter as it is... :-)
P.S. : I'm on OS 10.9.5