What are your favorite creatures to use animate dead on?
My personal favorite is the nightmare steed skeleton. Since it flew magically while alive, it retains that ability in death, and has an impressive fly speed of 90. Further, unlike a living mount, it never tires or needs to be fed.
Ogre Mage works great as a Skeleton, but Dragons and Hydras also work fantastically (and for that matter, Mariliths if you can find one that's not g!@~*!n summoned!) with large numbers of natural attacks.
Dragons ... be very aware that their kin not only dislike the practice of Necromancy as much as everyone else but they are capable of wiping out a whole town just to put on Skeleton to 'proper rest'. And then come back to sort your narrow pale ass out.
Hydras ... slow as dial-up, but very effective. The more HD they have, the more heads they have. Slap the Bloody Skeleton template on one, order it to protect a certain area and walk away. Being as it is Huge, you can even animate it and not put it under your control, just leave it as a sort of automated trap at the worst (in terms of environment) place in your fortress and listen for the screams as insipid heroes crawl through your narrow sewers, getting nice doses of diseases before running into a giant 12-headed snake skeleton that just won't die.
Ogre Mage ... it can fly, it's natural attacks are no slouch at this level and in a pinch your necromancer can climb into the rib-cage and hold on, directing the Ogre Mage to fly where you will it while claiming soft cover from the skeleton around you.
Marilith function the same as Hydras but are smaller, so best to hide them in a room where they're not going to be noticible in groups.
Flying Undead Skeletal Mounts .... hmmmm .... dammit now if you had said Fast Zombie we could have had a field day, but as it is, nothing in the first Pathfinder Beastiary comes to mind bar the Nightmare. Best of all a Nightmare doesn't give a two-copper fig about what happens to another Nightmare, so long as it profits from the result somehow.