1:3c 5th Fret Tuning

For this method, you'll still need to get your 6th string tuned to an E before starting. If your guitar is a little out of tune, but close, you can bring it in tune with itself at least. At any rate, you should learn to use the 5th Fret method. It will be useful at some point.

Here's how it works (assuming the 6th string is in tune, or close):
1) Fret the low E (6th) string at the 5th fret. The note you get is an A. Match the open 5th string to that pitch.
2) Fret the 5th string at the 5th fret. This gives you a D. Use it to get the 4th (D) string in tune.
3) Do the same thing on the 4th string to get a G and tune the 3rd string to match.
4) Fret the 3rd string at the 4th fret to get the B for the 2nd string.
5) Fret the 2nd string at the 5th fret to get the high E and tune the 1st string.

Once you have done this (and know a chord or two) play a chord to check intonation. An E chord works well for this. If it's not right, keep trying.

So, what are the problems with the 5th Fret method? Your low E string first has to be in tune, and you again need to rely on your ears. And lets face it, some ears are better than others.