The Setup

To achieve what you want, you'll simply have to wire all the light circuits in parallel off the common of the 3-way. Basically instead of a light on the common, you'll have light circuits. Something like this.

Following this scheme, each single pole switch will control the lights in a single area. While the whole circuit, is controlled by the 3-way switches. This way, if the 3-ways are OFF all the lights will be off. If the 3-ways are ON, the individual single pole switches will determine which lights are on.

The down side

While this configuration is possible, it may be confusing to any future owners of the home. This may also cause problems if the area is ever finished and actually divided into separate spaces, since a somebody could potentially be lost in the dark.

Code compliance

I'm not sure at this point whether or not this setup is code compliant, but a quick call to your local government should yield the answer. I will continue to review the National Electrical Code (NEC), to determine if there are any sections that would not allow a setup like this. If I find any restrictions, I will update this section of the answer.

_{If any others happen to know any codes that might apply here, please post the code section as a comment.}

That could be a split bus panel, meaning that there are two sets of power distribution buses. It used to be allowed by something called the "6 handle rule" (which allowed up to six of them in a service panel) back when circuit breakers cost a small fortune.

They were wired like this:

And might look like this:
Note the gap in the breaker buses at center where there are no breakers, but you can see heavy black wires connecting to the right end of the secondary buses.

The cables from the meter connect at right (which would conventionally be the top of the panel) and feeds the six double breakers. Five of them feed directly to heavy loads: range, water heater, dryer, baseboard heaters, etc. The top-left double ganged breaker feeds the second bus in the left half of the photo.

In this configuration, any circuit fed from the lower bus would be shut off if either its own breaker were switched off, or the feed breaker—which also shuts off almost everything in the building.