Broad layers are things like "the English version" and "the Spanish version". Every page in the collection should be translated into both languages. There are also clusters, which can be big, like PlanetMath and PlanetPhysics, for example. These clusters can intersect at various points, but the relationships (as I see them currently) are mostly local. Local relationships also exist between related elements of the same collection (e.g. two PM encyclopedia pages) or an element of one collection and its attachments (for instance, a PM page and the corrections that relate to that page).
I'm finding that broad layers are important in a number of ways in the projects discussed here. Sometimes they are important for building a project (e.g. collecting info for HDM by creating a computational layer of PM). Sometimes we would want to make the layers less directly related, for example, if every page on PP linked to the related pages on PM, or vice versa; we would have something resembling layers, but they wouldn't lie right above one another.
See also Literate programming and Free Math for another take on this whole thing.