For the most part I tend to approach custom fields from a workflow by workflow angle. The more workflows I can deprecate and delete, the fewer fields I'll have to look at. So if faced with thousands, and no automation of any sort, I would probably look for evidence that something hasn't been used in 2 years (or whatever number feels right to you). The fact that a form hasn't been used in the past 2 years would be a huge red flag. If a form was only used once a year, I would still question why.
By approaching it one workflow at a time, you can group your red flags. If a workflow has one red flag, they likely have more. It's unusual for a workflow to only have one custom form they don't use, and it's somewhat likely that this may indicate the entire workflow can be removed (which means multiple objects, followed then by their forms, templates, teams, roles, etc.)
I've also noticed a few times that sometimes people like to create a v2 or v3 of their custom form, so sometimes it's possible to audit and replace the older v1-2 versions outright (or with a bit of cleanup)
** Remember to check your field list to see whether reports are using the fields you're about to delete. These reports can likely also be deleted (in fact any report not viewed in the past 18 months can usually be deleted)
