Wood thaumaturgists would be able to shape and influence nature. These would be a good candidate for the people growing the elven treehouses, and they'd have influence over the growth of other plants as well. They could grow vines to conceal doors, grow trees to massive size before they're chopped down for extra wood, improve the general growing quality of certain areas and farms and obvious create magic-shaped wooden items.
Now, to make sure these guys aren't just "better than ledgendary" versions of the crafts they can work, they'd have to be balanced. I'd say the best option is to make their work go slower than that of a normal crafter at the same skill level, but having them producing a better product. Also, they shouldn't start being able to do every single thing they'll eventually be able to do, or at least not very well. And of course, there probably wouldn't be a whole lot of these guys running around, and if you wanted more than one each at a fortress you'd definitely have to jump through some hoops lure one there.
Other types of thaumaturgists could include alchemists, who could go beyond simply create potions to doing things like turning lead into gold, creating homonculuses and other assorted beasties. Rune-carvers who impart magical properties to items could fall in this category, but at the same time I'd like to allow hedge and high magicians to carve runes sometimes too. There's probably more types of magical professions that could qualify as thaumaturgists, and if anyone has any ideas let's hear 'em.
High magic is the real powerful stuff. Where hedge magic is like alpha testing, teasing something great out of an imperfect yet mysterious system, high magic is like programming: communing with vast, unknowable forces and spending hours upon hours staring at arcane languages that can drive an ordinary moral mad.
High magicians don't really go out adventuring much. These are the guys that spend all their time building either their worldly or otherworldly power. They've often studies under a mentor or at a school for decades, and they've attained the benefit of it. They draw their power from the same source as hedge wizards and thaumaturgists, but they've fully learned to commune with and command with the source of their power. While they sometimes may make deals with demons or gods for power, they only use that power to channel more power from an elemental source.
As stated, high wizards are extremely powerful, and as a consequence they rarely serve anyone. You're unlikely to ever have a high wizard come to live at your base, though one might attack, or visit to provide services. At the same time, if you're playing a high wizard, you're pretty much going to have to be building a tower or other community rather than looting tombs. While a high magician would definitely participate on the world stage and might even swear alliance or service to nations, they're fairly independant entities that serve their own interests, whatever that may be.
I'm not really going to get much into what high wizards would do in "wizard tower" mode, because I know that's a long way off. But presumably they'd be able to create their own magical servants and attract other servants, as well as cast spells, ala Dungeon Keeper.
Random magic thoughts
Magic should be somewhat sparse. While these things are pretty cool, it shouldn't overwhelm gameplay. It might even be a good idea to prevent players from micromanaging exactly what their magic-users do, except for thaumaturgists who have such a specific economic purpose. There also shouldn't be mages running everwhere all the time demanding your attention.
When they cast spells, magic-users should face a risk of physical or mental harm, as should their targets. Using magic should cause the caster to become tired, hungry and thirsty, and spells that require the target’s body to do something, (such as a cure wounds spell or polymorphing,) should as well. Casting too much without eating, drinking and sleeping should lead to death, if side-effects don’t kill you first.
Laypeople should gain some skill in religious magic if they participate in it frequently. Occasionally, a deity may bless or curse a follower, or grant them great magical powers. Divine/Infernal magic should be fairly unpredictable, as should natural, animal and ghost spirits.
Things like necromancy should be contained mostly in religious magic, though there could be specific cases where a skeleton could be animated without specifically using unholy energy, or however undead are made.
I definitely didn't address everything, even in a post this long. I also probably missed quite a few spelling and grammatical errors. Forgive me.
Toady, you've made a really amazing game and I'm really looking forward to the future. I've been having a great time testing.