Three sets of lights, turned on together or separately
Cheap and simple doesn't work with what you're asking. The most you could probably do is keep the "master" switch for each section and wire another switch on each light which, at most, would only be able to toggle select lights individually if the "master" switch is in the on position.

The only other way to obtain what you're looking for is with electronically controlled switches and relays which, exactly how it sounds, is not simple nor cheap.