How about a puzzle that involves reaching a switch that's located somewhere that can only be reached by flying? A platform floating in mid-air, perhaps, or a ledge on a wall that's covered by a continuously flowing, magically re-supplied stream of slippery goo that makes Climb checks unfeasible.
Depending on what other powers your characters possess, they would need to recruit something that's able to fly up there for them - and there's some corpses of winged creatures in the room, or perhaps in the previous room, requiring them to go back and fetch the bodies of monsters they just had to defeat in combat, 'dungeon recycling' if you will.
Winged zombies can fly, but if the party's Animate Dead spell gives them skeletons, they would need a creature that had a magical flying ability in life - winged skeletons can't fly. Again, depending on their caster level, a Beholder Skeleton might be out of their HD range, but a Tiny little Beholderkin Skeleton would certainly be a possibility.
Conversely, you could have a puzzle involving flying undead that have already been animated, and are winging around in pre-determined flight patterns inside a large cavern. Beneath them, there are pressure plates, but they're placed on top of large pillars jutting out of a deep chasm. The pressure plates are too far away for the PCs to simply throw stuff at them, so they'll need to use Halt Undead to make one of the undead (giant zombie owls, perhaps, to stick with a theme of 'only those possessed of Wisdom may pass through here') land on a pressure plate; this triggers a mechanism that deploys a bridge across the chasm, which the PCs can use to go cross. Even trickier, the PC will have to time their spell just right (perhaps requiring a Dexterity check, a Spellcrafting skill check, or an Initiative check) to get the undead to land where they want. Perhaps one of the previous puzzles rewarded the PCs with a potion that boosts their speed, or Spellcrafting skill, which would help them in this situation. Or you could allow one of the other PCs with a high Dexterity to act as a 'spotter' to the spellcaster's 'sniper' - e.g. the party Rogue could an aid another action to act as a look-out, giving the spellcaster a bonus to their roll. You might allow the caster to make a Concentration check, if that gives them better odds, since this situation could be seen as "the spellcaster is just about to cast the spell, but is holding back the arcane energies until the Rogue says 'Go!'".
Or you might be a nice GM and just let them hold a readied action to cast the spell until the undead is in the right position. The best solution is probably to let the PCs come up with their own strategy for timing the spell, and the roll with it (and for it).
Alternative: Chamber full of tiny zombie owls, and one of them is carrying a key that the PCs need to unlock the next door. The door might be completely bereft of keyholes of doorhandles, but there is a sign with the embossed letters:
THE WISDOM THAT STILL LINGERS HERE
UNLOCKS YOUR MIND FROM ALL ITS FEARS
SMALL IN SIZE YET GREAT INDEED
WILL BRING THE ANSWERS THAT YOU NEED
The PCs can make Spot checks to find the zombie owl that's different from the others - a glint of metal from the item it's carrying, perhaps. The DC shouldn't be too high, even if there's lots of owls; flying zombies are clumsy, according to the rules, nowhere near as agile as living birds. They then need to cast Halt Undead to make it stop flying, at which point it will, of course, plummet to the ground, allowing them to collect the key.
Elaborating on KRyan's great idea to use the Animated Undead's invulnerability to several threats that would be lethal to living creatures, you could have a puzzle with Death Rays that need to be blocked to allow the PCs to pass. For example, the PCs just passed through a chamber that had lots of cute little woodland creatures in it, perhaps with a puzzle for a Druid or a Ranger. Some of the animals follow the PCs into the next chamber, frolicking happily around the most nature-friendly characters - and then stumble directly into the path of a sickly green laser beam and drops to the ground, stone cold dead. This way, the PCs are immediately alerted to the danger that the beams present. (Of course, if you want to be a not-quite-killer GM, you could have the beams do some kind of non-lethal stunning or Sleep effect.)
If the players are unaware of the fact that undead creatures are immune to death effects, let them make a Knowledge skill check with a low DC to find out; after all, the chamber is probably decked out with a skull-and-bones motif, the floor littered with the decayed remains of previous visitors.
Alternative: If your players are familiar with 'Harry Potter and the Half-Blood Prince', they probably remember the puzzle with a large font filled with dangerous liquid that had to be emptied, before Dumbledore and Harry could get the locket on the bottom; however, the only way to empty the vessel of its enchanted contents was by drinking it. This time, if the players are smart, they could just Animate some Dead and let THEM do the drinking.