Honestly, I don't expect many people to actually know what the difference between a vocoder and auto-tune is. Not like Scratch Magazine didn't do a whole article on the differences about a year ago, just saying. I think wikipedia is to blame.

Auto-tune is a plug-in made by Antares, which is used for pitch correction. While it's best used sparingly, on parts where a vocalist like J. Lo, for example, might not be able to keep her pitch steady for an entire verse or what have you, rappers and singers these days just run their main line of vocals through it in excess and you get robot-like audio. I think people assume it's the same thing as a vocoder because it uses a form of vocoding to achieve its process, but not it's not actual vocoder itself, nor does it produce the same harmonic results.

A vocoder is something totally different than auto-tune, and it's not a Roger Troutman talk box either, which is another mistake people seem to make. Without getting too deep into signal flow, a vocoder takes a signal- say you've got a microphone plugged into a synthesizer like the Roland V-Synth GT. The signal that comes through that microphone (you singing, rapping, chanting, whatever) is sent to the series of oscillators and filters which create the synthesizer's sounds (now mixed with your vocals), which you can play through the keyboard or along with the keyboard. However you alter those filters and oscillators, that will change the resulting sound.

The best recent example of I've heard of a vocoder in action has been on will.i.am's album, on a song called "Impatient." Listen to this song all the way to the end to hear the vocoder in all its glory. Notice how it sounds NOTHING like the auto-tuned vocals that people have been confusing with vocoder for the past two years or so.

will.i.am- "Impatient"

Class dismissed.