Hail Caesar, the ancient-to-medieval wargames rules from Warlord Games. The mechanics are heavily based on their 18th-19th century rules, Black Powder, with variations to better reflect pre-gunpowder warfare.
There is much that I like about these rule sets, not least the fact that they assume that games are played between gentlemen (or gentlewomen) and friends, and not between cads, bounders and mortal enemies. Therefore, much of the pettifoggery that inevitably leads to tiresome metagaming and rules-lawery is avoided in favour of keeping things moving and everyone having a jolly good time. They are, as much as any wargame can be, non-competitive, and I like that.
Something that all of Warlord Games' rules do is to provide lists of special features and abilities that can be applied over the base rules, to differentiate specific troop-types. They may, for example, make troops more or less difficult to shake or disrupt, or make them more ferocious in the charge while less enduring should that charge fail to destroy the enemy. The lists, as the authors point out, are exemplary rather than definitive, and players are encouraged to create their own where they deem them necessary.
The beauty of this system is that it can be trivially adapted to fantasy wargaming in the vein of Hordes of the Things* simply by creating appropriate troop abilities and applying them as required. Most things can be achieved with minimal alteration of existing ability classes, but not all — flying troops, for example, are not something the authors of Hail Caesar really felt the need to address, there being a paucity of them in ancient times (as far as we know).
Wizards on the battlefield are slightly problematic — but only slightly; for the most part they can be dealt with using existing mechanisms. In game terms, any sort of attack spell (fireballs, calling down the lightning, and so forth) are really nothing more than a more spectacular form of artillery fire, and can be dealt with as such. Things get a little bit trickier if you want to incorporate things like illusions, mind control and so forth, and care needs to be taken that such abilities aren't too earth-shakingly powerful (unless you actually want the game to degenerate into a contest between opposing wizards).
Taking mind control spells as an example: I would suggest that an attempt to take over an opposing general could be thwarted by a successful 2d6 Command Roll, on the theory that the better the general, the greater his strength of will and so forth. If the mind control is successful, the player can then issue his own orders through his puppet-general for a period determined by a d6 roll: if 1-3 is rolled, one round. Two rounds if 4 or 5 is rolled, and three rounds on a 6. Mind control is automatically stopped if the wizard unit takes any casualties.
Fear spells could make troops more vulnerable to becoming shaken and breaking either by temporarily reducing their Morale score, or by inflicting "casualties" to the same effect. Fanatical or brainless troops might be immune to fear effects.
Undead troops like skeletons and zombies are something that would require careful handling, lest they become unstoppable death-juggernauts. They probably should have a morale effect on their foes, and they would fight until destroyed rather than running away, but just how far to go with these things I'm unsure of — it needs some pretty thorough play-testing I think.
These few examples show how easy it would be to adapt the game to whatever flavour of fantasy you prefer.
The key to building any fantasy wargaming adaptation to Hail Caesar is, in the end, the agreement of all concerned. If your wargaming mates agree, then go for it and try it out. If they don't, then make whatever modifications are necessary and renegotiate the situation as friends, not as adversaries. The whole point of the game is, after all, to have fun with toy soldiers.
Phil Barker of WRG has made the 2nd Edition Hordes of the Things rules available for free PDF download (for personal use only).