Well, may be some day in the future there would be an OSX version. Perhaps some one here could share some info on other converters which are available for OSX. Good luck!
If you're on Windows, FormatFactory is excellent, it handles almost all codecs and containers with an easy to use GUI.
I've heard MediaCoder is good too, but I've never used it.
Otherwise, there are the multiplatforms, VLC, makemkv, Handbrake, , and FFmpeg.
They all have their disadvantages, Handbrake and makemkv are extremely limited in the codecs and containers they will output. VLC doesn't handle batch jobs particularly well and it doesn't have support for variable or average bitrate encoding. FFmpeg requires one to be comfortable with the command line, though there are GUI frontends, but they usually hide much of the functionality.
My recommendation is to learn how to use FFmpeg with the codecs you output to frequently - some codecs like faac use tags that differ from it's recommended standards.
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