I don't even like using guitar tuners like the ones on Guitar Rig, TH2 etc. They drive me nuts. You obsess over getting that little green light exactly in the middle. And of course the pitch fluctuates a little from the attack of the note to the sustain so I'm never sure I've gotten it right. Besides which, tuning the open strings perfectly isn't always the best way to tune a guitar because of the inherent intonation problems that all guitars have, there are ways of tuning which are better.
I like to use a 440Hz tuning fork which I tune the A string's 12th fret harmonic to. Next I tune the 7th fret of the D string to that harmonic. I then tune the 2nd fret of the G string the same way. I then tune the B string with the 2nd fret of the A string, and the high E at the 5th fret with the A string 12th harmonic again. I then tune the low E string with the 7th fret harmonic of the A string.
The point of all this is to tune all of the strings using one string as a reference, the A string. I started tuning like this when I played classical, because I almost went mad over the fact that chords sounded great on the lower frets while sounding "out" on the higher frets, or vice versa. This method of tuning seems to even things out more. Works for me anyway.