This article only addresses standard tuning: EADGBE: Een Aap Die Graag Bananen Eet. The thicker the string, the less it gets out of tune. That's why it can be handy to start tuning with the low E string first, for changes are that it isn't much out of tune anyway. The basic goal with tuning the guitar, is that the strings are in tune with one another. However, with the advent of tunings apps for mobile phones, and cheap tuning devices, it's very easy to tune a guitar absolutely, meaning that the tones of the strings correspond with the exact tone of that note. That comes handy when playing with other people together.
Some ways to tune the guitar:
- Through the fifth frets: The fifth (and once fourth) fret of a string should have the same tonehight as the next string
- Harmonic tuning (flageolet) → Wrong
- Absolute frequencies: That's how tuner apps work.
Standard tuning frequencies
- E: 82 Hz
- A: 110 Hz
- D: 147 Hz
- G: 196 Hz
- B: 247 Hz
- E: 330 Hz
Finally figured out why the B-string is tuned relatively lower, compaired to the other strings: 
This gap is carried through on the last string. E.g.:
- The D-string is 10 semitones higher than the high E-string
- The highe E-string is 9 semitiones higher than the G-string.
- https://play.google.com/store/apps/details?id=org.cohortor.gstrings - gStrings, guitar tuning app for Android
- http://www.ehow.com/info-tip_8033248_different-hz-tunings-guitar.html - Standard tuning frequencies
- http://www.wikihow.com/Tune-a-Guitar - Many tips