You'll need a slew of magical traps ... especially teleport traps. They were originally used to reduce walking about the school of magic, but now will confuse any adventuring party. Some areas might only be reachable through using the right combination of teleporters.
For real deadliness, there could be open (or sealed) portals to other planes ... or even the Land Beyond the Magic Mirror.
Undead familliars roam the halls with their undead wizard masters.
Perhaps they don't even know that the building exists, to begin with -- it's cursed to be invisible until the power is turned off (cursed with the dying breath of the undead wizard who runs the place) -- all the locals know is that nothing grows in the dead space beyond the wall, and none who venture there ever return.
Lots of animated objects, still going about their tasks ... brooms, kitchen implements. Perhaps some are intelligent (Beauty and the Beast, anyone) and are happy/threatened to see living beings again.
An extremely powerful demon is still trapped in his pentegram; the wizard who summoned him dead before giving the dismissal (or else the demon roams the halls, trapped within the building).
Doors that only open to voice commands, with no other visible means of opening. Most doors are arcane locked, anyway.
There's graffiti on the walls in the students' area in arcane marks, perhaps leaving special clues.
The usual explosive runes and symbol traps.
Perhaps the ghosts/spirits/corpses of psat wizards, forever doomed to repeat the last tasks they performed in life before the guild was cursed/trapped/destroyed.
It becomes a murder mystery as the story unfolds ... a betrayal of the master by his star pupil.