The basic tonal qualitites of any given wood are dependent largely on the density of the wood. For example, the softer or less dense the wood, the darker or fatter the tone produced by an instrument built from that wood. This applies to necks as well, and the density of the neck wood, as well as the fretboard, will effect the tone of the instrument.
Mahogany is a softer wood than Maple, so Mahogany will produce a darker or fatter tone. Mahogany is the primary neck and body wood used in the construction of the most famous of all rock n roll guitars, the Gibson Les Paul. The tone acheived by the set-neck construction coupled with the Mahogany/Maple wood choice is among the most recognizable in rock music.
Maple is a very hard, dense wood. Maple is used for making baseball bats. The tone it produces when used to build a guitar is bright and airy. Bolt-on gutiars and neck-through-body guitars overwhelmingly utilize Maple for the neck. A neck-through-body guitar built from Maple is virtually indestructible.
Maple necks are usually paired with bodies or wings made of softer woods like Alder, Basswood, Poplar, or Mahogany. The softer tone woods tend to temper the brightness of the Maple to create a more desireable overall range of tones.