A few ideas, tjedge:
Great Wonders
Glantri - the School of Magic, obviously, but somehow you should include the concept of the Nucleus of the Spheres. It's central to Glantri. No Nucleus, no Glantri. Whether you do it as a resource that is only in one spot or a wonder, it ought to be represented somehow.
Thyatis - The Arena.
Ylaruam - there's a big university in Ylaruam, can't remember the name of it but it is fairly important, or you could do a Wonder based on Ylaruam's history the way they do Darwin's Voyage in the normal version of the game, I have the book and will look more into it if you like.
Alfheim - Tree of Life
Five Shires - the Blackflame
Minrothad - I'm not sure what it's called but the sea elves have some clan relic similar to the Tree of Life but not the same thing. I'll look this up too and post it later.
Unique Units
Ethengar - the Ethengar use mounted archers almost exclusively, they are have a very powerful army.
Glantri - a Wizard? There's nothing really unique about Glantri's army per se.
Darokin - Uses very fast, lightly armoured troops. I would think some kind of elite cavalry or fast, advanced foot troops would be appropriate. The way the army is described it sounds like a Renaissance type army with alot of pikemen, light armour but still a steel breastplate, rapiers, etc. You might not be too bad off just giving them a musketeer, although that's not part of the official material, for the purposes of the game it doesn't go against the 'flavour' of Darokin.
Minrothad - the Clipper Ship.
Thyatis - The elite of the Thyatian military is the Air Fleet of Retebius, which ride all sorts of flying mounts, primarily Griffons. This is supposedly the largest and most powerful of all the "air forces" in Mystara, it just doesn't have as much range as the countries with airships.
Minrothad - the Minroth Clippership. Very very fast.
Ierendi - the Steamship. Slow, but easily the most powerful seagoing vessels in Mystara.
Northern Reaches - Longships maybe or Berserkers, something with a Viking flavour
Karameikos - the elite military of the Grand Duchy is the Elvenguard.
Shadowelves - the elite military of the Shadowelves are Skinwing Riders (sort of like pterodactyls)
Orcs of Thar - obviously, orcs, but you might want to include War Machines as well. These are big siege platforms, mounted with catapults and a ram and ballistae etc.
I'll get back to you with more when I have time to look it up.
Btw, what versions of civ3 will this work with? I don't have Conquests.