After reading most of this thread I have to say that I have experienced most of the same things. However, a few comments made are only half-true.
For one thing, ALL 12-tone instruments are tempered, not just the guitar, and not just fretted instruments. If you have a chat with a piano tuner he will probably tell you that the notes get slightly sharper as you go up from middle C and slightly flatter as you go down from middle C.
Use a tuner, and get every note in tune. Play the open A chord that we all learn in the beginning...
The C#, (2nd fret of B string) will be HORRIBLY sharp!! But that's really "in tune" if you play the C# note in the tuner. The scale is just not perfect, so you do some adjusting or you live with it..... or you develop an outrageous vibrato!!! LOL
My recommendation is to buy a tuning fork. Most guitar shops will have an "E" for about 5 or 6 dollars, and just practice tuning the guitar with a variety of methods. I use the 12th and 7th fret harmonics on adjacent strings method, and just dial it in by ear. Even the best tuners have flaws, and the training you get from this will be valuable. If my guitar is perfectly in tune, it messes up my singing anyway......[/quote]