I know this topic like the back of my hand. Consider the following (for solid-body electrics; jazz boxes and acoustics are different due to the construction):

1. Pickups are microphonic so the vibration of different wood combinations do have an effect.

2. The denser the wood (or the type of wood), the higher the resonant frequency. The thickness of the wood also affects the resonant frequency. For example, the back wood on violins are tuned, preferably to high-F.

3. The combination of different woods on a guitar is necessary as some parts need to be stronger (high density, high resonant frequency) and some parts made of softer wood to balance out the resonant frequency. The preferable resonant frequency for a guitar? Beats me.
BTW, when I say resonant frequency I'm also referring to multiples of it. So to be accurate, it's resonant frequencies. And too much emphasis on a single frequency would give you.... tadaa, feedback.

4. So now onto the woods. It's widely acknowledge that the holy grail of tonewoods is the black korina. White korina is not as good, though it's still better than all the other woods. The cheapest tonewood that sounds great (and I don't mean relatively) is alder.

5. Mahogany is a good tonewood especially with a maple top. The maple top has to be at least 1/4" (at it's thickest) to make a tone difference. Anything less is purely cosmetic.

6. The construction of a guitar also helps in transferring the vibration from neck to body. The cheapest and most effective way is the bolt-on design due to direct contact of wood (neck) to wood (body); the cons: big ugly heel. I can talk more about construction but I won't dwell deeper for now.

7. Densest wood you all probably know would be ebony, least... basswood.
That's all I can think of right now...