I checked up on my website at Google Analytics and realized that most visitors end up here by Googling something along the lines of “FormatFactory vs Mediacoder” and end up at the article about Mediacoder or the article about FormatFactory, either really has an comparison. Here is a brief comparison.
Features: Both are about the same here.
Ease of Use: MediaCoder throws down all the settings in one place and offers many advanced options. FormatFactory is better for the run-of-the-mill computer user who wants to convert one file to another format.
If you know a lot about codecs and want to not only change the format of a file, but squeeze out the best size:quality ratio, you should lean toward Mediacoder. I was using MediaCoder for a while, but it is just easier, in my opinion to use FormatFactory. You can read my guides and determine which is easier for yourself.