This is the full procedure I use for tuning :
1) Adjust the tuning on the A string, until its 5th fret harmonic matches the pitch of a A-440Hz tuning fork. (If you use an electronic tuner, use it to tune the low E string up to pitch and proceed directly to Step 3.)
2) Adjust the tuning on the low E string, until its 5th fret harmonic matches the pitch of the A string's 7th fret harmonic.
3) Finely adjust the tuning of the low E string until it is slightly *sharper* and more pleasant to the ears. This step is vital, and a keen musical ear is required here.
4) Adjust the tuning on the high E string, until its open string pitch matches pitch of the low E string's 5th fret harmonic.
5) Adjust the tuning on the D string, until the pitch of the D string 2nd fret matches the pitch of the low E string's 12th fret harmonic.
6) Adjust the tuning on the B string, until the pitch of the B string 3rd fret matches the pitch of the D string's 12th fret harmonic.
7) Adjust the tuning on the G string, until the pitch of the G string 7th fret matches the pitch of the D string's 12th fret harmonic.
8) Adjust the tuning on the A string, until the pitch of the A string's 12th fret harmonic matches that of the G string 2nd fret.
The above steps might seem a little complicated when written down, but it is actually very simple and straightforward. Do give it a try, it really does make a noticeable difference. This method of tuning is also known as "power tuning".
Be sure to read through the link above for more information.