In this screenshot, you can see that there are only 479 records with data in the "911" custom field, which represents 0.4 of my total lead records in the org. How valuable is this field? This is the type of question that you can begin to ask your users. To get more detailed information, click on the ID for the record. In this case it's FS-250. You now have more granular information about this field and its usage.
You can now see when the field was first used, when it was last used and the number of days since it was last used. This is the kind of information that will allow you to build a case for deprecating a field.
I know it seems like a lot of work, but sometimes you need to get down in the weeds to make sure that you keep your org clean. This very valuable information for a system admin. In this post I have given you a small glimpse on one of the ways you can start tackling your "custom fields gone wild". Hopefully this has given you a good starting point to begin your clean up. Keep in mind that this is an ongoing process. This is not a "one and done". Good luck.