Run a filter for "Custom field is not empty"?
No, the filter is the way to get the list of usage, which you can then do all sorts of other stuff with.
The issue navigator alone will tell you something about project usage, but how elese you use it really depends on exactly what you're looking for.
A couple of easy reports - create a new dashboard, and add two gadgets (both using your filter). I think a "filter statistics" gadget, with "project" as the field to group by answers the basic question you've asked, but you might actually find a "Two dimensional statistics" a lot more useful if you choose "project" and "custom field" - it will tell you which prjects are using what values and how much.e
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