Do you use Cubase as your DAW?
When u say autotune, i take it as u mean antares auto-tune.
Personally, I feel that antares auto-tune is the best.
I will rank them as: Autotune, Melodyne then variaudio.
Autotune allows the best tuning of a note I feel. Most of the time, a bad singer tends to not be able to hold its note. To me, 1 of the biggest problems is when the singer goes seriously flat. He or she start on the right note and then slowly drifts off into about 1 or 2 semitones flat(could be more). Which is really hard to correct using the basic autotune functions. And autotune allows you to redraw the pitch back, and other nice functions such as vibrato, humanize. It is also much easier to use to create those electronic auto-tune vocals like t-pain kind. However, to me, autotune takes too long a time to tune a single note that is slightly off-tune, which means really low productivity. It is a real waste of time for me, unless you really have to deal with a very bad singer which I could have him or her work with a good vocal coach/producer instead.
Melodyne and Variaudio is really similar I would say. Variaudio is probably like a "lite version" of melodyne which would mean that melodyne has much more functions versus variaudio.
The difference between melodyne/variaudio and autotune in auto mode is that autotune pulls the pitch closer to the note of a scale while melodyne/variaudio shifts the pitch form to the note you want to go to. The sound is different because the resultant pitch form is different.
Melodyne is really good imo. Melodyne works really differently from auto-tune. Melodyne detects the pitch and then maps it out into a piano roll. If you arrange in a DAW, you would know what i mean. You could just shift the pitch easily up or down. And it sounds more realistic imo. You can also adjust the pitch drift. Melodyne allows you to pitch modulate, which you can use to create vibrato.
For me, I would choose melodyne or variaudio over antares autotune. To me, I will only use autotune to treat the vocals when i absolutely cannot use melodyne or variaudio to help it.
By the way, all 3 programs can be used to deal with instruments tuning etc as well.