Axes can be very good for character classes that cannot use "missile" weapons.
For instance, Kensai and Cavaliers cannot use missile weapons. However, I don't believe that a thrown axe (i.e. Rifthome +3 or Throwing axes) qualifies as a "missile" weapon. Therefore, those classes gain a quasi-missile weapon is they have axes (or hammers) that can be thrown.
Also, Berserkers cannot do any more than specialize in missile weapons. If you Grand Master in axes...I believe that those bonuses still apply when you throw the axe. Big-time bonuses...
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Now where did I leave that doughnut?!