I have used autotune with both cooledit 1.2 and 2 with no problems. I'm using version 3 right now. I haven't done a whole lot with it but it's worked fine every time i've called on it.
and don't be afraid to use it either! not only do people use these programs to make themselves sound like robots...alot of the newer pop sensations who couldn't really hold a note in the first place are depending on tools like this to stay in tune. I can hear it on alot of songs where the autotuner comes in....i don't care what kind of body you have and what dance moves you have..none of that matters when the cold ugly truth comes out of the speakers...
I could see using it instead of doing a punch on a performance I liked a lot but was a bit pitchy somewhere else in the track. Technology is a wonderful thing.