My entire music collection is encoded in FLAC (some 9000 tracks), and I transcode to MP3 often for my portable players and car. dBpowerAMP Music Converter
is my tool of choice. (You'll need the FLAC codec
And joint stereo does produce the best sound quality in MP3 encoding. Think in terms of bit efficiency. At a maximum bitrate of 320kbps, there are still a finite number of bits per second used to encode your music. You can use more bits than necessary to define stereo seperation (i.e., "full stereo") and less on actual sound quality; OR you can use only the bits required to define the stereo element just above the perceptual threshold (i.e., you won't hear any difference between JS and FS), and use the bits you've saved to improve actual sound quality.
This is why MP3 files using joint stereo do (or have the potential to) sound better than those using full stereo.