To use some of the non-undead creatures, just have the shadows lurking in some of the sights where the largest battles occured. The other, more out of the way places, could be haunted by other strange critters.
On that note, if you have the Draconomicon, a Skeletal dragon could be used in one of these situations. A Dracolich would work perfectly as well.
In a dark underground pool lurks an ancient Aboleth Wizard. Perhaps the PC's stumbling around in the dark awaken it and it sends some of its minions (undead maybe?) to spy. And with the way the leveling system works for creatures with large HD, the Aboleth could turn be a pretty decent spellcaster with not too high of a CR.
There's always room for Pudding. A Black Pudding could be lurking within an ancient armory, ravenous after years and years of no food. This is also the perfect time to make use of the greatest and most illogical monster ever... the Gelatinous Cube!
Rust Monsters and Xorn could have found their ways into the complex, searching for large veins of metal, gems, whatnot or large caches of treasure.
Perhaps some Cloakers as well...
Also, the
Tome of Horrors is a perfect book for decking out your dungeon with dangerous denizens. Lots of critters that fit well into the whole dungeon ecology thing.