There are some really powerful spells in Fire (Holy Pyre) and Astral (Solar Rays). Because you are most often fighting against lots of undead critters at once, the best bet is usually having your mages cast these. Marignon Witch Hunters are able to cast both, Theurgs can cast Solar Rays, etc. Herald Lance allows a non-mage commander to cast Solar Rays, and as such makes them many times more powerful against undead. Flambeaus would cast Holy Pyre, but they are probably too expensive to make only to be used against masses of undead. If you want to be ready if an undead SC appears, having Flambeau and a tough commander won't hurt. It gives 3x damage to undead...
All kinds of priests are also powerful against undead. Most often having lots of cheap independent Priests works quite well, e.g. Jotunheim shouldn't start churning out Jotun Godes (240 or something gp each) just to get level 3 priests...
Against hordes of mindless undead lead by few commanders, use mind-affecting spells. The only targets in the battlefield will be the mages leading the undead...
Against undead SCs, use Maggots. It's a Nature spell, and can be quite deadly.
One of the best single magic paths against undead is Death. Few Sauromancers casting Wither Bones are a sight to behold.