From their site, OmniTuner is:

A versatile tuner for a variety of instruments.
A real, microphone-based guitar tuner and much much more.

- A sophisticated pitch-detection engine
- A fretboard mode that helps you tune stringed instruments, including banjo, mandolin, and many more.
- Multiple guitar tunings
- Easy-to-use hands-free interface
You may better know it as its jailbroken buddy, Funiculus. Essentially, its the same app, but OmniTuner is way prettier.

I like this one a lot, I play guitar on stage at least twice a week, and all the time at home. Obviously I need to stay in tune, and I use OmniTuner (and Funiculus before that) all the time to do so. It works great with the iPhone microphone, even in the back room of wherever I'm playing, with A/C blasting loudly and folks talking.

The fretboard is a cool feature, and also where you can change the tuning. OmniTuner supports a bunch of common guitar tunings, which you can easily switch back and forth between. There's also a notation view which shows you the note on a musical staff.

All in all, well worth the $4.99, and built by a member of MMi to boot. I use this one daily.