Here's what we've decided to do, since we're a pretty small company...
We're going to have very few collections. Our primary collection is called "Production" and we'll have a few others called "Playground", "Proof of Concepts", and "Educational References".
The reason for doing it this way is that our rules/workflow/data needed for work items/etc. for how we handle things is very consistent company-wide and rather than recreating this customized configuration for many different collections, we'll just use different projects for that. The collections will be for when we need to go by different rules (for example, there will probably be no check-in requirements in the "Playground" collection but there obviously will be for the "Production" collection.
So in case it's not obvious at this point, it sounds like a different project per customer is what I'm suggesting for you. But of course, it really depends on your company, how large you are, how similar your project management style is (if you do CMMI for some projects and agile for some others, you might want to separate them), and some other needs.