I am in the TOC camp. Primarily for the reason:
As a developer, i only want to maintain one application.
As a user, I want to be presented with the same interface everytime.
The one off/one layer apps are annoying. Every one is different. Maintenance is a nightmare. User experience is terrible.
The whole point of GIS is bringing desperate data together. That means choices.
Oh, and most of all
The user should decide what layers to display, not the developer.
/my (not so humble) opinion