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You have to work through each function that an add-on provides and look at the config or logs, or activity.
Add-ons can do so many different things, there's no way to know where they all might be being used, and the methods to work out their usage vary wildly.
If, for example, an add-on creates a custom field type, it's easy - run a search for "custom field of that type is not empty". But if it provides a report, you're going to have to read access logs to see if people are using it. If it's a workflow function, you need to read all your workflows (although a search for the plugin key in an xml backup is usually easier), and then there are "compound" plugins that do several things. A good example would be JMWF, Scriptrunner, Powerscripts - a project might be using them for a workflow function, a field, a process, etc etc etc. And then you have the non-project items - for example, a listener is project independent living in global configuration, but may well have settings that say "only listen to these 4 projects"
The most reliable, but potentially evil method is simple though. Disable the add-on. See who screams.
