Selective eletrical shutoff throughout house without tripping breakers?

Is the second breaker panel run as a sub panel off the main breaker panel? Your main breaker could be going out in the older panel, they usually go out 1 leg at a time, meaning half the house would have power, and the other half wouldn't. You can test this by finding a 240 outlet, like the drier or electric range, and connect a voltage meter between the 2 hot legs. If it reads 120 volts during your outage, that could be your problem. It could also be one leg of the transformer on the electric pole as well. You can test this by removing the cover of the older breaker panel, and being very careful not to touch anything else, touch your voltage meter to the main lugs of the 2 hot legs coming into the home. If it reads anything less than 240 volts there, then the problem is outside and you should talk to the power company. Your description of the problem sounds like you're loosing 1 leg of power.