From years of working in a music shop and also setting up guitars I am pretty good at getting them in pitch by ear. I know I don't have perfect pitch, but just like everyone else was saying, you get a song into your mind that you know perfectly and you check out the tuning using that.
When I started playing it was either pitch pipes or a tuning fork. Pitch pipes were too much of a pain for me, the tuning fork is a lot better. Once you are used to using it, you have the 440Hz in your mind and can hear it when you need it (Keep 100+ guitars in tune every day for 3 years and you wil hear it too!). I still have one on the bench when I am working, though I don't really use it too much. When I am settig up guitars now I use a Peterson Virtual Strobe tuner, though I do the initial tuning by ear. Also, I always check with several open chords to see.
The guitar is not a perfectly tuned instrument anyway, this is why there are all the different methods of tuning the open strings to keep the intonation better. I know that if you take 5 guitarists who do tune with their ears, and then you have each take a guitar tuned by someone else, they will make subtle changes to the tuning. This oesn't mean that the guitars were tuned wrong in the first place, it more reflects what the style is that the guitarist will play more.
I think that there are pros and cons to an auto tuner, just the same as there are pros and cons to electronic tuners. How many people who use an electronic tuner use the sound option? If you are only tuning visually, then it is the same as using an auto tuner.
