I keep a small screw driver handy in the case for fine tuning intonation. The 12th frett (actave) harmonic should match the fretted note. If it doesn't, the string should be longer to bring the fretted note down a bit in pitch and vise vera. The harmonic note is always pure, but the position where it rings best will change slightly.
It's pretty easy to tell if a string is really bad (usually caused by messing with the setup) and sort it out. To do a bangup job you need a decent tuner and want to balance other issues as mentioned in the above post.
edit: Just a warning, if you haven't done much of this, it's pretty easy to make it worse than before, strip screws etc...