Magic in computer games tends to be a matter of casting a spell, handling its effects, and being done with it. That has never seemed right to me. Magic should be rare, hard to control, weird, mysterious, and full of consequences. How many games do you know that meet more than one of those criteria?
Rare. Making magic rare is really easy, thankfully. The dev notes mention being able to change this at world generation, which is good enough for me.
Hard to Control. Making magic hard to control in Fortress mode is very simple. Dwarves are already somewhat hard to control, and Dwarves who get enough magical power can become semi-noble. Their labors list changes to a bunch of magic-related ones, and they stop performing other labors. However, they get weird moods very frequently, for any skill. Your mage might commandeer the carpenter's workshop, create a strange artifact, and leave without becoming a carpenter of any kind. These artifacts have all the random attributes of normal artifacts, none of the quality, and only a small chance of having magical properties. When magic users aren't busy being somewhat of a nuisance, they spend most of their time contemplating in whatever profound locations your fortress offers. Occasionally, they go perform the task their labors tell them they should be doing. Occasionally.
Weird. You need side effects. Tons of them. One fun method of doing this is a subject/verb/object matrix. Subjects and objects would be any objects in the game. Verb would be things like "becomes" and "floats to" and "repels". Each magic user has one random subject, verb, or object that is constant for them. Each task for that magic user has another one of the three chosen randomly as constant. Every time a magic user does something magical, the last of the three is chosen randomly, and the effect happens to the nearest two of the appropriate object. Maybe you got a healer who got "Dwarf repels x". Sometimes his patients start repelling arrows, and that's great. Other times his patients start repelling water, and that's not so great. If he starts casting some other kind of spell, all bets are off: is it "dwarf" or "repels" that's constant for him?
Mysterious. Those side effects don't have to be instant. They might have an onset delay of years. If you use lots of magic, some side effects might happen for no apparent reason at all.
Consequences. Generally, I'm an advocate of magic annoying some supernatural entity or another. Maybe nature hates magic, and using too much will make the trees march to your fortress and try to tear it down. Maybe demons think magic is theirs, and they'll climb out of hell to get to your magic users. Or maybe the side effect system you use is bad enough on its own.
[ December 05, 2007: Message edited by: SquashMonster ]