In the first
Dwarf Fortress Talk Toady mentioned that there is a problem with implementing magic-users in a fort, and still keep magic mysterious. Problem being that a magic user might simply become a gold dispenser, or perform other stuff that might become mundane in the end through extended use, and knowledge of capabilities.
The solution, I'm thinking, might be to make the magic-user a useful noble-type inhabitant, beyond the control of the player, kinda like the dungeon master is currently. So the magic-user would decide when to use magic, and to keep it mysterious, he probably wouldn't do it all that much. During everyday humdrum, he might just produce useful alchemical stuff, lob fireballs at invaders, and other mundane magic (or maybe not, if you consider lobbing fireballs at invaders too mundane). But once in a while, he'll get mysterious. Maybe, when the fortress is starving, he announces that he will summon food for everyone, and does so. A one-time event, and something that you can't rely on. Maybe when a baby gets born, he blesses the child. Maybe when a large army shows up, he cracks the earth into a chasm which they all fall into. Maybe he demands steel and quarts, and withdraws to craft a magical axe. In the lifetime of a fortress, there might only pop up five of these events or something. With a large enough list, he'd always be able to whip out something surprising. Something.. magical
There are some stuff which he can't decide on his own. Say, if he suddenly decides that he want to magically strengthen the fortress walls against siege engines. If he were to do that himself, he'd probably just end up enchanting the stretch of wall between the dining room and the privies or something. But in that case, you might have him ask you where (or whether) you want the stuff. "Sire, the fortresses' walls could bear strengthening. Where would you want me to apply my powers?", "Sire, I notice we have chambers on opposite sides of the bottomless chasm, do you wish me to craft a bridge of pure force?", "Sire, I have bound a fire elemental to my will. Which chamber do you wish it to guard?" Stuff like that.
Now, some of you might disagree with the magic I used in examples. Some might disagree that dwarves should have magic users. But this is about how to implement magic users, not necessarily dwarven ones. So even if you think dwarves shouldn't have magic users, would this be a good way to implement human and elven magic users (when we get to control those civilizations)?