Kigo Video Converter is a free video converter for the Mac. There is one thing that I particularly like about this converter, and I noticed it the first time I ran it: it looks like a native Mac app. That might sound like it isn't a big deal, but it is for me. The application is incredibly intuitive and that is because of its interface. You can simply drag and drop files to the interface to add them to your conversion queue. That is how a Mac app is supposed to be: effective and good-looking.
Although the output format support is limited in this converter, it makes up for that with a nice YouTube video downloader that works great and is incredibly fast. The supported output formats are AVI, FLV, 3GP, 3G2, MP4, and WMV, among others.
I tested this app by converting an MKV file into MP4. Kigo Video Converter opened and converted the file very well. It took a minute and a half to do it, which isn't slow, but isn't fast either. The resulting file was of good quality. I noticed that Kigo kept the subtitle track of the MKV file and it hard-coded those subs into the MP4 file, which is a very nice feature. You can also load an SRT file to use this feature.
Kigo Video Converter is a free app. There is a more feature-rich version, but at a price.