My method is to get one string (usually A) in tune with something else (another guitar / tuning fork etc). Then.. before I strat,Incidentall by "Harmonic note" in the explanation below I mean put finger ona string without fretting it, and pluck the string so you get a harmonic note instewad of the fretted one.
Play a harmonic note on 5th fret of bottom E This should be the same note as the harmonic on 7th fret of A string Whork up the strings with this, so 5th fret harmonic of a string = 7th fret of next string up.
This obviously doens't work between the G and B string, so I tend to tune to the G string with this method, then play the 3rd fret on the B and play the G and B (a fifth interval) - it's quite easy to pick up the "sweet spot" where it's in tune. A bit of amp distortion can help here. Then do the B and E strings as before.
What I like about this method is that apart from the B string, it uses no frets so if you've got a wobble of intonation somewhere in your guitar, as many of mey earlier cheaper ones did, then it sidesteps the issue and you end up with the guitar tuned to itself regardless of what the frets do.
I run through that then play a G, an A and a D just to check all the bits of the guitar sound ok together.
I always tune up to the note, never down. Tuning from a higher note down leaves some residual looseness in the string meaning it might go out of tune pretty quickly.
The only drawback with this is that it makes quite a noise, especially if it's an electric guitar. Best turn amp down ...
But my main method is to use one of these : http://www.dv247.com/studio-equipment/zoom-g1n-guitar-pedal-includes-power-supplly--69803
They're kind of ok ish as effects units (you get what you pay for ...) but the built-in tuner is super-accurate and really easy to use. It displays the note you're tuned nearest to with a spinning 0 (one segmend of LED screeen moving) - left = you're flat, right = you're sharp, and an 8 when you're spot on. Superb.