Special CasesThere are a few types of creatures that require a special degree of analysis and discussion.
Creatures With Class LevelsWhile most effects of classes are lost, proficiencies and special qualities that enhance melee and ranged attacks remain. Movement modes and ability score adjustments will usually be lost due to being special qualities, as will any natural attacks due to being special attacks.
Creatures with class levels will frequently have higher than normal Strength and Dexterity scores due to using the basic or elite arrays.
True DragonsDragons come in way too many varieties to cover, most of which make really good skeletons and zombies. They universally have 10 Dex, though, so skeletons always have AC 12 or 13, depending on size. Lots of natural armor, so zombies get high AC despite that. Universally great movement modes and natural attacks, although oddly they have only moderate Strength scores for their HD. Also, dragons have their own special way of being animated (see Draconomicon's Skeletal Dragon and Zombie Dragon templates) that make them even more powerful.
HydrasAmazing skeletons and the undisputed king of zombies. Short version is that whenever they'd get one attack, they get to bite with all of their heads. As far as straight up combat goes, this completely negates the biggest downside of zombies' limited actions, the lack of full attacks.
The nature of a hydra's heads is a natural ability. It's neither a special attack nor a special quality. It's simply part of the monster. Hydras can attack with all their heads at no penalty, even if they move or charge during the round. More so than that, all of the heads' attacks are listed in the attack entry (separate from the full attack entry), which indicates what the hydra can do when it's given an opportunity to make a single attack (such as a standard action, at the end of a charge, on an attack of opportunity, etc.). There's also a bit about hydras using all of their heads for attacks of opportunity with the Combat Reflexes feat, which confuses the matter since they lose the feat, but they're still totally awesome even if they only get one attack on AoOs (they probably still get one attack per head, though).
A hydra's heads can also be attacked independently, they regrow, and they can be sealed with fire or acid (or cold, for pyrohydras). Heads regrowing seems like exactly the sort of thing that would be lost when a hydra is animated as an undead creature, having lost both fast healing and, due to being mindless undead, natural healing as well. Technically, it still keeps that thing, despite all that, which is a bit weird. Since almost nobody ever uses sundering, it's really not something worth the effort to get into or worry about.
Also worth mentioning are pyro- and cryohydras. Pyrohydras have the fire subtype, while cryohydras have the cold subtype. Otherwise, as skeletons and zombies, they're identical to regular hydras. If you're making skeletons, pyrohydras are obviously superior, having fire and cold immunity. Hydras are still so damn good for skeletons and zombies that cryohydras, which add fire vulnerability for no gain, are still at the top end of the top tier for skeletons.
SwarmsSwarms are neat. They keep the swarm subtype, which is most of what makes a swarm awesome in the first place: nauseating distraction, swarm attacks, immunity or extreme resistance to conventional weaponry and targeted attacks, etc. Unfortunately, they're really hard to animate.
Animate dead just doesn't do it for a number of reasons. First, it targets a specific number of creatures (it may not have an upper bound, but it still targets only what you designate). Second, a swarm doesn't leave a corpse behind most of the time to even animate. Reducing a swarm to 0 hp doesn't even kill it, it just makes the swarm break up. If you want it to leave a corpse, you need something like a death effect that straight up kills it without reducing it to 0 hp.
If you want a skeleton or zombie swarm, you have to get creative. You need some sort of area of effect spell or ability that kills creatures, and one that animates the dead. The
Fell Animate feat applied to an AoE death effect like
cloudkill or
circle of death can do it.
If you can pull it off, you get a great undead minion. It's just really, really hard to do so, and by the time you can the swarm might not be worth the effort.
Skeletal Structures and Natural Attacks That Require FleshNot all creatures can be animated as skeletons and zombies, and even then, some natural attacks might be lost to skeletons. Aside from the obvious things like oozes, elementals, and blobs of light like Lantern Archons and Will o' Wisps, here are a few cases that I had to do some research on. And by that I mean spend 5 minutes on Wikipedia.
- Octopi, squids, and their larger and/or magical counterparts (including krakens) don't really have have skeletal structures. Squids (and by extension krakens) have some cartillage about them which might be enough. Check with your DM or your local marine biologist.
- Tentacles and cephalopod arms don't generally have any sort of skeletal structure. Therefore, skeletons will lose those attacks. This is a real shame, because krakens and giant squids have tons of natural attacks and great strength to back them up. This also affects several other creatures, such as aboleths, carrion crawlers, chokers, displacer beasts, gricks, mind flayers, and otyughs.
Anybody who actually knows anything about the relevant parts of biology, feel free to correct me. Please do, really. I feel like I'm just this side of guessing here.