Thanks for the wishes guys. I am smiling today!
Ralf has it right - the guitar (and ANY instruments where pitch of notes are fixed, like a piano for example) is designed around equal tempered tuning. But in equal temperament, certain intervals are not quite what the ear likes to hear.
Why? Well, in Just Intonation (what the ear likes to hear, think barbershop quartets) the correct pitch of each note depends on what key we're playing in. But to do that correctly on a guitar we would have to retune the guitar if we change key and possibly adjust the fret positions. It's totally impractical on, say, a piano which has 88 keys and 240 strings!
So we need a compromise - we'll use a 12 note scale, divided so the notes match in every key (which is why it's called equal tempered). We don't mind a few chords sounding just a little bit off, provided all chords sound equally good (or bad) in every key. It means that some chords don't sound as perfect as we like but we don't have to retune every time we change key.
It's important to note this - that's how guitars and pianos and saxophones and harmonicas etc are actually constructed. 99% of all recorded popular music was played on instruments that were designed that way! And every tuner that you use for your guitar displays pitch according to equal tempered tuning.
For people with sensitive ears, even a well-tuned guitar can have some chords that sound a little off. When we try to adjust the tuning to improve one chord, we can end up putting some other chords even further out. It's important that we accept the compromise and learn to live with the sound of well-tuned guitar. It's not a barbershop quartet, nor should it sound like one! Pianos are equal tempered and they sound fine doing (almost) exactly what a guitar is supposed to do!
One last note for JMD - when we use distortion we are actually adding harmonics to the sound. Those harmonics don't always conform to equal tempered tuning so chord forms with three or more different notes quickly start to clash. It sounds very messy, particularly when we get away from fifth and fourths (power chords, basically). If people want a distorted sound with a specific tonality, IMO, the best options are simple two-note intervals of root-third, third-fifth, etc., usually with one of those notes in the octave above, and their inversions. Basically try any two notes out of a standard chord shape and see what the result is like. But resist the temptation to re-tune! There are other instruments there and you have to be in tune with them too!
