The problem with a Auto Tune you can't see in real time the A/F ratio like the wide band commander does, the Wideband Commander also allows for full data logging of the A/F ratio.
The Wideband Commander does not build your fuel map like the auto tune does. The Auto Tune can only be used with a PCV, the wide band commander can be used on any bike or car no matter what type of fuel injection or carby you have.
Wideband Commander
http://www.hardracing.com/misc/wideband.htm
Auto Tune
http://www.powercommander.com/powercommander/Products/AutoTune/powercommander_autotune.aspx
If I was to buy a new A/F meter I would go for a Wideband Commander 2, the new one is a auto tune as well as A/F ratio meter to see real time A/F ratio, it can't data log like the Wideband commander 1 which I have.
http://www.dynojetwb2.com/