Missing computer?

You might be able to use traceroute to figure out which router it's connected to.

After finding a router, you can figure out what switches are behind that router.

Once you've found the switch, you can use the switch to identify the MAC address associated with the system, and the port.

Once you've found the port, use your wiring diagrams (if you have a generally-accurate inventory, I imagine you have these as well) or just trace the cable to the destination.

I actually had this problem myself ten years ago. The PC in question was an OS/2 box. It was running server processes, so there was no user session; in fact there was not even a display or mouse hooked up to the thing. There was a (mini)keyboard, but that was simply so the thing would reboot after power failures or what have you. When time came to move, no one could find the damned thing, there was no documentation, and there was no one left from the era who know what it even looked like, let alone where it was.

We used echo location (ie. beeping in a loop), and wrote a script that opened and closed the CD tray remotely every 30 seconds. Eventually, it was found in a not-quite-abandoned wiring "closet" underneath a staircase. It was totally caked in dust, and looked like the closet had not been opened in years.

It was the opening and closing of the CD door that gave it away; one of the office girls heard this repeated thumping noise (the CD tray was hitting the side wall) and reported it as a possible animal incursion (not unusual; squirrels and raccoons were always trying to get into the building). The maintenance people called us when they found the source of the noise was a misbehaving PC.