The table above is from a slide in Atlassian CEO Scott Farquhar's presentation about the upcoming JIRA 5 Release. It shows some details about how organizations use JIRA, and agrees with what I see at CustomWare's clients.
1087 projects, 1231 custom fields, 361 workflows - so how do their JIRA administrators manage all that?
There's the Hundred Tab Problem to deal with, where changing a scheme has to be done through the UI for each project in turn. And then there's the bigger problem of not being able to see how schemes differ.
I think the answer is that they must have their JIRA configuration thoroughly documented and always make the changes in a staging server first.