My 2 cents/pence on Tonewood So I thought I would take a stab at addressing one of the most debated subjects in the guitar community for both players and builders. Of course I can only give my opinion based on my experiences with guitars I have played, built and woods I have used and worked with.
Overview An electric guitar works because the pickups, which contain magnets, convert the vibration of the metal strings as they affect the magnetic field, into sound (very basically). Now the big argument is how do the woods the guitar is built out of affect that relationship, if at all. In an acoustic guitar, the woods make a huge difference in the sound of the instrument, this is due to the varying grain of woods and how dense they are. The wood vibrates along with the strings and the vibration of the woods along with the strings and how the woods interact with each other gives that acoustic guitar its own tone. This is why cheaper acoustics do not sound as nice or as resonant as more high end acoustics made with superior pieces of wood. A case could also be made that no acoustic guitar will ever sound the same as another acoustic guitar as it's impossible for them to be made from the same piece of wood.
Trees are grown, not man made so therefore each tree and even different parts of the same tree will have variations in grain and density which in my opinion is what makes working with wood so interesting; nature is random, but it is also why some guitars with the same specifications as another guitar don't quite sound as good for some reason! Weight = good? Many people think that a heavy guitar will have better tone than a light guitar, this argument is generally based on older Les Paul's sounding good subjectively compared with lighter guitars (which is easy as old les pauls weigh the same as small house). These people have obviously never played a blackmachine or a strandberg (or one of my guitars) as weight doesn't affect the tone as much as the density.
Of course density means a heavier wood, but Les Pauls are thick guitars, being 50mm or more, whereas blackmachine and my guitars are usually around 35-37mm in thickness and you lose lots of weight but no noticeable difference in the sound of the instrument. Perhaps older Les Pauls sound better than newer Les Pauls due to using mahogany that grew naturally and for a long time and wasn't harvested as a fairly young tree, a case could also be made for differences in building techniques etc.
Construction of the guitar is an important factor to consider in the tone of an instrument. Bolt on guitars are generally brighter than through neck instruments. They also offer the opportunity to experiment with how much difference neck woods can make to tone as you could change a strat from a maple to a rosewood neck and there will be tonal differences. Through neck guitars generally have much better sustain than a bolt on guitar, so if someone believes the wood isn't vibrating and affecting the tone why would this be the case?
As the vibration of the strings is transferred to the through neck guitar which in turn causes the whole instrument to vibrate which in turn allows the strings to vibrate for longer creating longer sustain. Of course this can also be achieved with well built bolt on guitars with a tight neck pocket and on set neck guitars.
Thick or thin
Finishing of a guitar can also affect the overall tone of the instrument and it is generally accepted that adding a thick lacquer can negatively affect the tone of the guitar. John Mayer's "black one" fender strat started out with that idea in mind as in his words he “wanted the wood to resonate more” and that guitar sounds great. However, having a beat up guitar is not what everyone wants especially from a custom guitar, so lacquer serves a great purpose for protecting the wood despite its potential tonal downside. Oiling a guitar is basically the opposite of the lacquer where the wood can resonate a lot more freely, but taking a ding goes directly to the wood.
The pickups and electronics are probably the largest part of the cake that is your guitar tone (they're the sponge). This is why pickup companies are doing so well, it is so easy to achieve a great tone for your instrument by simply swapping the pickups. The tonewood debate does however raise some issues when it comes to pickup demoing but I will broach that subject at a later date. The electronics also play a large part in the pickups sound as well. Essentially the clearest way to hear how your pickup sounds is by wiring it straight to the jack socket as there aren't any other components in the way as it were.
As soon as you introduce volume and tone pots or a switch, the electronic signal from the pickup is affected in some way. Pots also have a +/- acceptable variance of 10% so the pot may say 500k but it could be as low as 450k or as high as 550k which can drastically affect the tone. Generally I like to use the Bareknuckle 550k CTS pots as they consistently sound great to me and maybe that is because they are always going to be more than the recommended 500k for humbuckers rather than ever being below that number. Final Thoughts I would argue that as much as the pickups are doing the bulk of the “tone” creation in an electric guitar, as they literally pick up the vibrations from the strings, the vibrations do not stop at the nut or bridge of the guitar and will be transferred into the woods of the guitar. This all of course happens at the speed of sound and will therefore affect the overall tone of the instrument. Changing the pickups in your guitar is the easiest and most apparent way to change the tone of your instrument. However when ordering a custom guitar or looking at buying a new guitar, considering wood type, construction and finishing of the guitar all play a factor in how the guitar will sound as well.
I think you have to look at an electric guitar as more than what each element is doing and look at it as a whole. Every single part of the guitar and how well it is put together, will affect how the guitar sounds. If a guitar was a ferrari (not that i've ever driven one, I can dream), then the pickups would be the engine, the part which has the biggest effect on the car overall, but how the engine works with the rest of the car is what makes the ferrari great, you can swap out the engine and it would still be a ferrari, but it wouldn't be the same as before and it is the same as pickups in a guitar, they are the largest factor affecting the tone, but not the only factor and how well the guitar is built and what the rest of the guitar is made out of will also affect the sound of the instrument. So now you just have to worry about your amp, cab and pedals...