An army marches on its stomach. The world-devouring necromancer's primary enemy is logistics: how to get enough humanoids to power your bodyworks in a short enough time to prevent massive unified retaliation by the world's more annoyable wizards and clerics.

While consuming the souls of bunnies (as suggested by a previous edit) is both cute and delightful, bunnies lack two critical prerequisites: the humanoid type and an intelligence score.

The central plan here is the idea of the "Wraith Pit" (freely stolen from a previous game I was in.) Wraiths have the ability:

Wraiths have the ability:

Create Spawn (Su) Any humanoid slain by a wraith becomes a wraith in 1d4 rounds. Its body remains intact and inanimate, but its spirit is torn free from its corpse and transformed. Spawn are under the command of the wraith that created them and remain enslaved until its death. They do not possess any of the abilities they had in life.

Now, the optimal undead horde will have three requisites: the ability to ignore the controlled HD limit but still retain control, the ability to create spawn, and incorporeality.

The biggest problem with the optimal undead horde is growing them properly. The second biggest problem is a sudden loss of control. The third biggest problem is "getting there firstest with the mostest."

The first route is the Full Metal Alchemist. Build a utopian city (preferably an arcology with exactly 5 foot thick floors). Provide free services and a wonderful way of life. Criminals, are, of course, put in "eternal sleep." When the city reaches a useful size, let loose your primary wraiths and consume it. The downside is that "utopia with slight evil at its core" doesn't provide "hordes of undead" until the final step.

The second route is the spectre/wraith/shadow horde. The spectres are nice because a hit from them bestows two negative levels, which suggests a round or two to kill a commoner. In a deep sewer, desecrated, with a shrine to... $evilGuy, haul the homeless, travelling merchants, and other people no one will miss. In that place, your incorporeal undead should nom on the living. Specifically, your "leader" of the city should turn people into wraiths/shadows/spectres. By having a very flat hierarchy, you introduce a flaw into your system (single point of failure) but make it very hard for groups of your minions to be uncontrolled. If you're going this route, you'll want to target every city of a kingdom simultaneously. To do this, you'll need to have the Necrotic Cyst and the ability to cast Necrotic Tumor. That way, you can turn high-ranking people inside the prisons, government, and clerical orders before starting this plan. Then it's a simple matter of funneling the city's undesirables to the desecrated zone until you have, roughly, a spectre per household. Then pull the trigger as the sun goes down. After a few minutes, you'll have converted most of the kingdom. So long as you've necrotic tumored enough clerics and wizards, anyone who's managed to resist can get slaughtered by their "friends." If doing this on a long term plan, don't forget to build hospitals, orphanages, and tenements.

For this sort of style of play, the direct confrontation with the BBEG will likely be somewhat anticlimactic. While rebuking an honour guard of undead is cool, your earliest bet will be via metamorphic transfer.

For this sort of behind-the-scenes "do gooder" builder of hospitals, orphanages, prisons, and spectre factories, I'd probably recommend a spell-to-power erudite 6/ur-priest 2/psychic theurge 6 (the levels after this get tricky, but that's not the point.) Erudite is horrible at adventuring, but great at casting a number of really tricky spells per day. During preparation, you'll be travelling around, planting necrotic cysts in everyone at level 3. The erudite is mainly to get you access to any arcane spells. The bard spell list in particular is nice for social scmoozing and sneaking about. It's also necessary to get manifester level 5th for metamorphic transfer. You may want to dip your first level into binder (for naberius, always useful when working around undead and in social situations), tenebrous apostate, and the divine version of anima mage. In any event, you'll want to be a necropolitan, and use alter self at level 5 to, combined with metamorphic transfer, turn into a shadow (and) Wraith, and start those armies breeding slowly. Search this list for things under 5HD that can create spawn, ensure that they create spawn that are under their control, and go to town. Metamorphosis at 13th level will open up other spawning options, as ur-priest gives you the various divine animation spells that are also handy.

Level 13 also gives you necrotic tumor, so you can ripen all of the cysts you've (and your followers) have been planting for years. All it really takes is time, and access to the minds of spellcasters.

Level 14 allows you to metamorph into a Mohrg, which will allow you to animate as many zombie rabbits as you desire. Since there's no cap, It's an excellent way to build a huge army of rotting fur and cuteness. There are benefits here, too. Zombie rabbits (and other cute animals) will cause people to leave the countryside and increase the population of cities. Therefore, you can use your "zombie threat" to both scare off villages, lull your enemies into a false sense of security (who wants to be hired to vanquish zombie rabbits?), and concentrate your primary food where you want it. With that said, there's nothing stopping you from doing the same to dragons, but the world takes zombie dragons far more seriously.

You'll also want a cadre of significantly less stealthy crypt chanters. Getting the first one will be very tricky. With a stretch (a very big one) you can grab the mantled erudite ACF, take the natural world mantle, and use the suggested "substitute powers" pseudo-acf in minds-eye to swap earthquake for greater shapechange. Unfortunately, that will have to wait until level 19 for it to be of any utility. It might be worth dipping into a PrC which provides the animal domain, which allows you to get shapechange when the ur-priest reaches 9th level spells. (level 15-16, depending). Crypt chanters have an excellent chance of enthralling huge groups of organised opposition, and eventually converting them into more crypt chanters. You'd want to have a chorus of at least 4 of them before trying to convert any sizable forces, but if you have a brass band of them singing row-row-row your boat (with a portion stopping every round to reset the saving throws), they are exceptionally hard to beat. If you issue your forces with wands of dispel magic to dispel death wards, you can use quantity to wear down even the scariest of Pelor's clerics. (Beware the ablative zombie bunny hordes!)

Yes, it is possible

It is actually possible to obtain a permanent skeleton companion. That being said, it is a slightly convoluted process that is not without certain shortcomings. This method involves using two spells in conjunction:

Finger of Death

A humanoid killed by this spell rises at the start of your next turn as a zombie that is permanently under your command, following your verbal orders to the best of its ability.

True Polymorph

Choose one creature or nonmagical object that you can see within range. You transform that creature into a different creature ... If you concentrate on this spell for the full duration, the transformation becomes permanent. ... If you turn a creature into another kind of creature, the new form can be any kind you choose whose challenge rating is equal to or less than the target's. The target's game statistics, including mental ability scores, are replaced by the statistics of the new form. It retains its alignment and personality. ...

By now, you probably understand where I'm going with this. You would first start by using Finger of Death to create a normal zombie servant under your control. Next, you would use the True Polymorph spell to transform said zombie into a skeleton (which you can do because they are both challenge rating 1/4). Then you simply wait out the spell's duration, which makes the transformation permanent, and, since a transformed creature "retains its alignment and personality" you now have one permanent skeleton companion at your disposal.

In fact, using this method, you could create a permanent companion out of any creature of 1/4 challenge rating you may desire.

In Summary

Finger of Death + True Polymorph = permanent skeleton companion