Two things have happened; The polyurethane has yellowed over time and the wood has gained a patina. The only way to eliminate both of these is to sand till new wood and refinish. This is a lot of work and most likely wouldn't be practical.
If you decide to sand and refinish all of your wood ceilings, one room at a time is the best way to do it. Also, use a water based poly or acrylic urethane as the finish. These finishes resist yellowing.