I'm willing to guess that if you were to see the raw signal that came out of the guitar that you'd see a difference in tones. However, they are probably so slight, that the human ear might not be able to actually tell a difference because the electronics, strings, pickups, etc will make much more of a difference.
But if you took two identical guitars, one made of maple and one mahogany and played notes, I would have to assume there would be a small difference due to difference density of the wood.
This, good sir, I can agree with.
If you compared two guitars with all identical parts and identical body dimensions, but way different woods, there could be a bit of difference...to, like, a computer. But not a human.
To the person who mentioned that it did matter to neck (not fret) materials, Re: intonation and sustain...I also say, okay, plausible.
But to the 'lulz you noob' people...meh, keep drinking the koolaid. And I also gotta laught at people who want to say that [popular line of guitars] are known for sounding more [blank] than [other popular line of guitars]. Well, no shiz, because there is a lot that is different between them. Saying it's a function of body materials rather...well, everything else...that's silly.
ANYHOO...about tuners...try not to laugh here...but 'G Strings' for Android. It's quite fantastic. Doesn't even seem to matter how shitty the phone is...it somehow figures out the pitch and gets you pretty damn close.
If I plug into my preamp and use software (Amplitube), it's much more picky, and it becomes obvious than the phone app is doing some rounding to make it easier on you. But either way you go about it, the guitar still sounds in tune. I've even set up intonation with G Strings, and it did a pretty damn good job.