I agree with R. Shackleferd. I was thinking of a tuning fork before I got to his post. Except I use an E tuning fork; I don't know what frequency it vibrates at, but it's just easier for me. On an acoustic, I just tap the fork on something, and place the end on the body of the guitar- the tone will vibrate, and you can tune the high E and then the other strings accordingly. After all the strings are in tune, check the intonation of your guitar. If it's off, get it set-up properly. Oh, on an elctric guitar, I just hold the fork over one of the pickups. I use an E fork so I don't have to fret anything- yes, you can hit the A harmonic on the 5th fret A string; but I'm just giving a slightly different take on tuning.

I also agree that you should learn to tune manually before you get dependent on a pitch pipe or electronic tuner. But if I had to choose between the two, I'd trust the electronic tuner more, as the reed in a pitch pipe is subject to environmental conditions that can throw it flat or sharp.

After you're comfortable using the 5 fret tuning method, then I'd move onto tuning the various other methods, like harmonics, etc. But definitely make sure your guitar's intonation is proper- otherwise you can go nuts wondering why you can't get in tune. btdt! Can drive ya nuts.