(This is edited from an answer I posted to KeyMinor, a music Q&A site. They need more users!)

A lot of recordings end up slightly higher/lower than standardized pitch (I always called this “in the cracks” but don’t google it!), and this is the quickest way I’ve found to tune a guitar to them.  This method seems simplistic but has several advantages going for it:

• All strings are tuned to the same reference pitch, so there’s no accumulation of error as you move from string to string (and you can tune any of the top 5 in any order).
• The higher the frequency, the easier it is to notice the beat when two identical notes differ slightly in pitch. Matching high pitches yields lower error.
• All pitch matching is done with notes in the same octave; this also helps you notice the beat

Here it is.

1. Get string 1 (high E note) perfectly in tune with the recording so that you can play along with the song at various points on the string. Ideally the song will be in a key containing E because getting open E perfect is essential to this method. Check the 12th and 7th fret harmonics, too. If either sounds off, you know you’re not quite done.
2. Stop the recording and tune string 2 until its 5th fret matches string 1 open.
3. Tune string 3 until its 9th fret matches string 1 open.
4. Start the recording and play along using the strings you’ve tuned. If it’s off, return to step 1.
5. Stop the recording and tune string 4 until its 14th fret matches string 1 open. Get it as close as you can and check the caveats below.
6. Tune string 5 until its 7th fret harmonic matches string 1 open.
7. Tune string 6 until its 5th fret harmonic matches string 1 open.

Caveats:

• Your strings must be well-settled/worn in. You especially don’t want the high E to change pitch at all during tuning.
• If your D string has intonation problems, the 14th fret may not be in-tune with the lower frets. You may have to tune the D string using some other method at the end. You could, of course, have similar problems with the G and B strings if your intonation is really messed up.
• As you’re tuning, often you’ll get to a point where it seems perfect. Give it a little nudge more and often you’ll hear the two notes sink together, becoming one—that’s where you really want it.