Done a lot of research on this. Joint stereo should have a "better" sound when encoding MP3s with lower bit rates. Meaning 128 or under. Joint stereo is to take advantage of of similarities between the R and L channels and allows more bits to be used in other areas. There is less speration, but a better sound.
For high quality encoding, bitrates 160 and above joint stereo should NOT be used. As a matter of fact, it definately could have a negative effect, like distortion and loss of stereo seperation. There are are the bitrates to go around so you don't have to sacrifice the stereo seperation.
Bottom line, if I am encoding up to and including 128, I will use joint stereo. For 160 and above (where I normally encode), I use stereo
If you want some real scientific stuff, you can go to the Fraunhofer-Gesellschaft web site
http://www.iis.fhg.de/amm/techinf/layer3/. There is a good definition there of joint stereo which is
"Joint stereo coding takes advantage of the fact that both channels of a stereo channel pair contain far the same information. These stereophonic irrelevancies and redundancies are exploited to reduce the total bitrate. Joint stereo is used in cases where only low bitrates are available but stereo signals are desired. "