Try having a look at DBPowerAmp, its freeware for conversion and will convert to/from virtually any audio format as long as a plugin has been written to support that format
Its fast, and will happily run as a background task without hogging your entire system as a lot of conversion softwate wants to do
http://www.dbpoweramp.com
There is a plugin to convert from/to WMA, and the latest release now has MP3 support built-in, so you should have no problems converting WMA to MP3
I've tried searching for software to convert atrac3, but unless Sony releases the codec (which is very doubtful) or somebody creates a plugin for Sony Atrac3 then once you've converted any audio to that format and no longer have the original you're stuck with it
Unless you play back the audio through you're sound card and rip the actual audio while its playing, very slow, but its the only way if you no longer have the original tracks