I find it interesting that so many professional 'cough cough' producers and engineers can't actually pick out a pitch. Key proof of this occurs every time I hear tracks with autotune running wild. Here are some key tips for getting autotune right on your productions:
Use autotune as a tool to enhance a 'vocal performance' that has all other attributes intact. Autotune cannot fix phrasing, pronunciation and dynamic issues so take your time nailing the recording.
Autotune is also useful for monophonic instruments such as bass guitar. In fact I use it on a range of solo instruments, even brass.
Don't ever use autotune in 'auto' mode over a vocal. Even when used subtly the plug-in finds it hard to keep up with real time playback and jumps around the scale too much. This is at its worse when set chromatically, and often sends your vocal 'off key' that is often worse then it's original state. Instead use the plug-in in graphical mode. This allows you to edit phrase by phrase which helps keep audible pitch shifting to a minimum while retaining natural slides and vibrato.
Autotune uses a pitch shifting algorithm so don't use it to fix a note that is incorrect as the effects will become very obvious.
Graphical autotuning a whole track is a long process but is great for pop vocals as a perfectly tuned vocal will sit better in any track, especially if the instrumentation is programmed.
If you are going for that 'Akon' vocoder effect use midi notes playing a desired melody to trigger autotune. I would suggest using this after a vocal has been graphically autotuned.
Remember autotune is a gift to aid people who want to make great records and should be used only for the purpose of tweaking a great recording.