The undead can prove tough foes in RPG games, and they come in all kinds of makes and models. For the purposes of today's review, we should get into the mindset of the kinds that can be created as servants (animated skeletons and zombies) and those might be summoned and possibly controlled - especially the incorporeal types. Now, consider how those kinds of monsters could be made into integral parts of wards and traps. If spell energies and elemental creatures can be harnessed for magic items and other things, why not evil spirits and other undead?
Necromantic aspects can be strictly cosmetic, but it's probably a little more interesting to introduce some tweaks to game mechanics adapted straight from the RPGs rules for traps. D&D 3.0+ and the Pathfinder game provide stock and trade listings for all kinds of traps, which should make things rather easy than coming up with this stuff from scratch.
For example, instead of using the old spiked pit trap, why not use a pit filled with skeletal arms that attack hapless victims with the same kind of chances to hit and damage? If you juice it up, why not let the skeletal hazard make continuous attacks for anyone not making a hasty climb out of the pit? You should probably assign the skeletal components hit points or something to measure damage - most likely thanks to an area effect spell or holy energy. Alternately, you might just treat the skeletal bits as some kind of swarm (ie. like hordes of vermin) that inhabits a pit.
Think about the traps that release some kind of energy attack, such as fire or lightning. Why not use necrotic energy instead? This might have the effect of turning killed characters into some kind of undead. Alternately, it might just be a cool way to describe traps that make cold attacks, but be sure to mention that the assault on the characters has a creepy aura - ie. spirits whispering, grabbing, etc. This would certainly be the kind of trap that you could let the priests, holy warriors, or the studious use their Knowledge (Religion) skills to detect and disable/suppress harmful spirit wards.
If a trap normally requires a character to make a Fortitude or Reflex saving throw to withstand or dodge it, respectively, why not replace with an effect that requires a Will saving throw instead? As far as that goes, if the trap deals physical damage, I see no reason why a psychic attack couldn't do just that. Again, I can see malicious spiritual forces at work here, although this is great ground for those Cthulhu-minded.
Finally, let's think about hazards. Drowning is a dungeon-delving problem that can occur while swimming or if buried in enough debris. To avoid drowning, it requires Swimming checks and possibly Constitution checks if the hero goes under. Consider spiritual hazards - say a corridor of howling spirits - that requires Will save checks (or some relevant skill check), but maybe use Wisdom or Charisma checks to "hold their breath" while navigating or floundering the cursed hall.
The cover the right is from Dungeon #125 (back in 2004, I think). Mike Mearl's adventure, "The Three Faces of Evil," has an ultra creepy dungeon complex which features a section that messes with character's minds, if I recall correctly (maybe through an ever-present confusion spell effect). Lots of strange things going on in the adventure that the suggestions above would work well with. Recommended reading for anyone planning on writing an unholy temple adventure - you just can't beat the feeling Mearls evokes. One day I'll have to write a post of why this adventure is one of my all-time favorites.