http://www.proguitartuner.com/guitar-tuner/
Here are some tips:
Always go from a lower pitch up to the pitch you're aiming for. If your string is sharp and you tune down the string might have some slack in it, and will settle to a lower pitch.
Consider using the harmonics of the string to fine tune.
Starting with the E string, place your finger ever so lightly, directly over the 12th fret. The metal fret itself, not where your finger would go if you were playing the 12th note on the neck. Right after you pluck the string with your right hand, release the delicate pressure from your left hand and string will sing an octave of it's open tuning. When you play an open string the sound you hear is a combination of the base frequency (low note) and a combination of divisions of it.
This article explains it well:
http://music.stackexchange.com/questions/3849/how-do-harmonics-work
When you compare the harmonic from the 12th fret of the low E (6th string) with the harmonic on the 7th fret of the A (5th string) the difference between them will be in yo face. When you bring them together it will sound like one very clear note.
Having trouble getting a clear sound? You're not alone, don't give up. It's a matter of touch. If it doesn't work out despite your experimentation with pressure (so slight on the left hand) and timing pulling off, walk away from it for a while and try again later. You'll get it, tiger!
Check out the demonstration!
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Tune your E string to something accurate
Compare 12th and 7th frets of
6th string to 5th string
5th string to 4th string
4th string to 3rd string
to tune the 2nd string (B) , compare it to the 7th fret harmonic on the 6th string
and compare the 1st string (high E) to the 12th fret of the 6th (low E).
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This is all presuming that the intonation of your instrument is in good shape. When you attack the 12th fret of your 6th string does it sound perfectly in tune with the open note? If it sounds way off then you should adjust your intonation by making tiny alterations to individual string length on the bridge. Most of the time you can only do this on electric guitars. When luthiers make acoustic instruments they (hopefully) work hard to space the frets accurately and intonation shouldn't be a problem.
more on what's going on and how to check it here:
http://koivi.com/archives/guitar-intonation.php
If despite your best efforts your beater acoustic guitar won't tune up or stay in tune, all is not lost.
Strings don't sound good forever. Over time they can get stretched out, dirty, divoted, and will slip out of tune. Part of the problem could be that they weren't strung securely. When you put on a new set, set aside a good chunk of time so you can do it slowly and watch how they're catching. Spend some time stretching them out by hand too, this will go far in keeping them in tune. And as dorky as it seems, wiping down your guitar when you're done getting freaky with it will keep those strings alive much longer.
The machine heads (tuning posts) can become lose and slip over time and a replacement set is usually $20 at a music shop. Consider bringing your guitar in so you get the right ones.
Here's a decent video on stringing an acoustic, nylon string guitar.
http://www.youtube.com/watch?v=frLP_Sajd38
I stretch out my strings afterwards by slipping a sock on my hand and gently pulling (while securing the string at the nut or bridge with the other hand) and pressing down hard on the string over the nut and bridge. Do this a few times for each string, retuning each string after you stretch. Then repeat this strange ceremony 3 or 4 times and your fussy nylon strings should be good to go.
If your acoustic guitar still sounds wonky, just play it with conviction, no one cares!
http://www.youtube.com/watch?v=PK2HANwsUWg
