In fact, the B is generally the one out of tune, owing to the peculiar fact that, if you start with a note, takes its fifth, and the fifth of that, by the time you make it back around to the original pitch, you will in fact reach a pitch some 24 cents off of where the actual octave is, which will not sound good--so the frets are fudged a bit(this is, technically called tempering) so that the high e sounds where it should.

Unfortunately, this means that the open strings can't actually be tuned to perfect intervals, because then, when you tune that B a pure third above the G, it is going to be too high, so the b-e interval is going to sound a little squeezed, and the b-g(third fret on the e string) is going to be really awful because the g will be out of tune with the open G string.

At this point, it's going to seem like the problem is the e string, and when you try to tune it so it fits with the b and g strings, it is going to sound out of tune with the E and A, and that problem is going to be amplified by the fact that the low strings have octaves sounding.

To get the guitar (any guitar) in proper tune, you have to tune the A string first, then make sure that the A's on all the other strings are in perfect unison. This is somewhat complex, because it requires the use of harmonics, but it eliminates the need for electronic tuners, and you'll be amazed by the sound of the guitar when you're done.