Here is how I would do it: (without moving from my chair)
Check the CDR records (internal and external) and would filter each DN to see if it is used or not. I would have to check everyday for a month.
Then:
Call the numbers left to see if someone answers or if a device answers, I would do that for some time until I tried all of the numbers as many times I wish.
Then:
I would disable the ports left. Of course, I am the person who repairs all of the failures on my sites. So if someone is cut-off I know about it.
I already take a full TNB every month so after being disabled for a month. I proceed to out the TN left inactive.
I never did this, it is radical, but there is no way to know if there is an analogue phone plugged in, from sitting in my chair.
If you want to move from your chair there is ways... From the MDF you can use a device that will detect a phone or modem on the field side of each pair of wires. That means you have to deconnect each x-connect and test the field side with that device and re-connect it. And that methode won't give 100% results , still.
Go thru all of the wiring closets with a butt-set and you will be suprised how many dial-tones you will find on unused pairs.
Good Luck,
Cawho
PBX.Tech