According to my own experience using Video Converters, I am convinced that there is sofware called Pavtube Video Converter($35) powerful in converting.
I used it and found it supports plenty of video and audio formats such as MP4, 3GP, 3G2, AVI, MPG. MOV, MKV, AVI, FLV,AVCHD,TIVO, VOB, SWF, MP3, FLAC, OGG, WAV, AC3, M4A, MP3, WAV, etc.
Comparing with other converters, I prefer Pavtube one because of its fast conversion speed and its pretty good output video and audio whcih satisfy me.It is said that this software applies unique audio and video sync technology which can guarantee the audio and video match.
Of course, if u dont need so many formats, handbrake also is a good choice.