Guitar Tuner ($0.99) for iPad is kind of a cross between learning by ear and having a digital tuner. I like it because it encourages you to train your ear, at least more than using a tuner alone.
The interface is very nice, although it doesn't change to landscape orientation, which would be nice.
You can use the guitar string sound or a regular tone to tune your guitar. Just pluck the string and tune yours to the sound. You can also set the sound length to Hold, Free or Auto, depending on your preferences.
There are a number of alternate tunings available that will cover most users.