FFmpeg

Convert all WAV (or other format) files to MP3:(Edit)

Simple, easy, can be long to execute if library is large[1].

find -name "*.wav" -exec ffmpeg -i {} -acodec libmp3lame -ab 128k {}.mp3 \;

Convert all MOV (or other format) files to MP4:(Edit)

Quick and dirty, does not seem to affect quality too much[2].

find -name "*.mov" -exec ffmpeg -i {} -vcodec h264 -acodec mp2 {}.mp4 \;

Rotate Video when transcoding(Edit)

Add these arguments to the line, before the output filename[3]:

-vf "transpose=2,transpose=2"