The d20 SRD: http://www.d20srd.org/srd/monsters/skeleton.htm and http://www.d20srd.org/srd/monsters/zombie.htm
The Pet Store: Determining what to animate.
In the world of skeletons:
Movement Modes- The more, the better. Especially Flight. Remember they only get flight if they flew magically.
Natural Armor- Skeletons lose whatever great natural armor they had.
Ability Scores: Dexterity for the great skeleton archers who get improved init and a dex increase. Strength for the skeleton bruisers. Everything else is lost
Hit Dice- The nice part about skeletons, they don't double HD. This means your 10+ HD group is full of skeletons. No need to worry about this.
Special attacks-Sorry kiddo, you keep none of these.
Special Qualities- "A skeleton loses most special qualities of the base creature. It retains any extraordinary special qualities that improve its melee or ranged attacks." That leaves....almost nothing.
Subtypes- These can give you small benifits. One of the few things you can keep. Some resrictions apply.
Attacks- Strange wording here. Keep all proficiencies and natural attacks. The tricky part is that under attacks may be listed special attacks. Even if they are natural, we lose them.
In the bruiser world, fire giants are favored because of their fire subtype, Large size, and High Strength. This means a Skeleton Fire giant is immune to cold and fire. They also have an amazing amount of damage capability.
Fire Giant: 15 HD for 31 str, Dex 9 and large size(reach+larger weapon), and Fire Subtype
Efreeti: 10HD for 23 Str, Dex 17 and Large size, Fire subtype, and fly 40ft. Perfect
Ettin: 10HD for 23 Str, Dex 8 and Large size, and Superior Two-Weapon Fighting
Umber Hulk: 8HD for 23 Str, Dex 13, Large size and Burrow 20ft.
Bralani(Eladrin): 6 HD for 18 Str, Dex 18, Med size and fly 100ft. Perfect
Mephits: 3HD for Fly speeds, and Small size. The key here for low levels is that the natural weapons count as magic for overcoming damage reduction, they all have different elemental subtypes.
Wait, did I hear that right? Skeletons are known as great archers, but now we have a flying archer with fairly good dex. His HD are also low enough for the somewhat optimized necromancer! That's right folkes, an Efreeti is at least equal to an Ettin, maybe better depending on what you're looking for. Time to go even lower in levels. My suggestion is maybe take the Dijinni if you have to, but don't take the Janni. The Dijinni also has large size, less HD , but better dex than his cousin.
Skelton Mount(for the low levels)
With Nimble Bones, your created mount would have an extra 10ft. movement. Odds are you end up with a horse at best, easy to come by. BTW, Pounce is a special attack. That means that giant kitty skeleton won't teach the girl next door to play nice. For an animal, an elephant would be ideal, but that's CR eight and I don't think you'd still want it by the time you can kill it also, it kinda stands out(Hence the elephant in the room joke). Now, it would be great to have an octapus on land. Not as a mount, but for the Ink cloud, and maybe for the grapple.
Dire animals are all the rage. Since it isn't your "Animal Companion", you don't have to deal w/ Mr. Tier 1 Druid's limited selection problem. All of the following animals are large size for mount purposes and practicality. If you have any versions of Corpsecrafter, your undead mount will be better than the base version of the Druid's pet.
Dire Wolf: 6HD for 50ft. move, 25 Str, and 15 Dex
Dire Boar: 7HD for 40 ft. move, 27 Str, and 10 Dex
Dire Horse(MMII): 8HD for 60ft. move, 22 Str, and 13 Dex
Deinonychus(Dinosaur): 4HD for 60ft. move, 19 Str, and 15 Dex
Diprotodon(Dinosaur)(Sandstorm): 9HD for 40ft. Move, 10ft. Burrow, 27 Str and 10 Dex
Gambol(MMII): 8HD for 30ft. move, 15ft. Climb, 23 Str, and 18 Dex. Debatable if it keeps its Haste. If it does, this thing is extra blue.
Why is strength so important? Carrying capacity. Horrid Animals are great, even better than dire. But have fun trying to find one that doesn't have a druid owner. Unless you kill them both, animate one as a good undead(the druid) and his companion as a skeleton.
Others that may be campaign/ location/ luck dependant.
Forest Sloth(MMII): 14HD for 40ft. move, 40ft. brachiation, 60ft. Climb, 25 Str and 20 Dex
this thing has a high CR, but as a mount, it can get you anywhere on land. Just strap on really tight. May be a little overpriced HD wise, but depends how many HD you can animate. Also, it keeps all of its movment modes
Fleshraker Dinosaur: I take it you know what's so great, but remember, no special attacks.
Zombies are like everyone's cousin who is obsessed with football. They can be extremely enthusiastic, but are rather slow and limited.
Zombie hunting:
Speed: It's nice, you can keep flight but you get clumbsy flight instead. Unless you want some sad attempt at a flying mount, don't worry about this.
HD:
It doubles, so you're rather limited. At least this makes them good line men. Stick 'em in the front and let them take the damage instead.Abilities: Same as earlier, but Strength and Dex increase.
O how they suck. Partial actions only, and toughness...
Natural Armor: The ONLY thing zombies really have going for them. Get some good natural armor, it increases. Plus, you add the double HD. They're like living walls! That attack(occasionally).
Your options are limited. But, some still exist.
Hydra: Standard action for all attacks from its heads.
I would like some other suggestions on what other players find to be good skeletons or zombies. Please leave some note of why, and I'll add them to the list with credit to the original poster.
Using the Army
There are several forms of thought when it comes to using your minions. One of the most important things to note is fun. In a PARTY, you have to work with other players. Just like the game can lose its fun when NPC's do all the work, your minions shouldn't replace other players.(Unless you need to because there is no tank or such)
First off, we have the defensive position. This usually involves Zombies with high Natural armor and tower shield/ armor. The way to implement this option, is to put the undead on caster watching duty. Instead of having your tank stay behind and guard the squishies, you have the undead do it. Another option is using reach weapons, and the skeletons(Most likely large size) to have a wide threat area.
Our second, more popular option is archer style. A small group of skeleton archers can sit in the background near you, the casters, or on their own. If they are seperate from the rest of your party, it can cause your enemy to divide their forces. This is in effect battlefield control. The high dex skeletons are great when combined with longbows.
Next, we have our bruiser formation. In this form, you assist the tank with high damage. Good strength combined with large size can pull off great damage. Usually this means you'll be having one or two major minions. Remember keep one behind to protect you. Enjoy having meat shields that you can afford to lose.
Our last option is unique. You have to be a higher level and have awaken undead or create undead. The point in this form is to basically create a party of undead that work for you. Send them in seperatally as a distraction, or have them occupy your enemy's reinforcements. This form will allow your party to be unaffected by your extra members. Another benifit is that the DM will like the control over the challanges, allowing them to use the undead as plot power. The downside is that this will cause more danger to your undead and your pocketbook.
Equiping your minions
Here's the real problem. You're already spending 25 gp/ HD for the pets. So, why do you want to spend money on hum-dum meat shields? Well, your pets DO get natural attacks. The thing is, 1d6 slashing damage isn't that great, neither is the zombie's slam. Our real goal is to play to the strengths of our minions.
Longbow, Shortbow: These are great for skeletons, you may burn through arrows, but its worth it.
Longspear: This is good for AoO skeletons and large undead who already have reach.
Flail: Good damage to price, may want this for a large number of minions.
Greatsword: 2d6 damage and 50gp
Greataxe: 1d12 damage and 20gp this is slightly worse than the greatsword damage wise, but better price wise.
Javlin: 30ft. range and only 1gp. The Romans used these, why don't you?
But, the best option is simple. Let them keep their stuff. Odds are you are animating your former foes, so they come with their own gear. The trick is to maintain consistancy. Too many different weapons means even more book keeping. A good thought is to have at least two weapons for your minions.