I want to convert audio tracks of some video I have. These are mkv files, and I want to convert only the audio. The video codec is fine. I attempted to use VLC, but VLC added occasional blocking artifacts to the converted video. I am looking for free software.
ffmpeg will let you re-encode just the audio stream. It is freeware and very flexible.
If you use Linux, it's probably in your distribution's repositories. For Windows, try the WinFF GUI. I don't know how full featured it is, but the good news is you can run the included binary directly from cmd.exe.