House is two years old. Once last summer, and now lately, when running the A/C a humming noise begins to come from what seems to be the ductwork on top of the furnace. The sound can be heard throughout the house, but the compressor outside seems fine.
It takes several hours before the sound begins then becomes increasingly louder. If I turn the A/C off for several hours, it is quiet again, at least for a little while. There is also an air exchanger in this proximity. Any ideas?

May be a noise or vibration transmitted through the refrigerant piping, a/c may be building up a high head pressure have you washed the outside unit lately? Try it , can't hurt.

Thanks. I'll try that first. Any other ideas?

Some times a transformer will set up a vibration or humming sound , the transformer is in the furnace.