Some advance research can help you know if you want to travel with a carry-on bag only (to save a baggage fee) or to bring your own lunch rather than buy one at the airport or on the plane. Some websites, including Travelocity offer a comparison chart on baggage fees at major airlines.
Your calculations can even extend to costs after your flight lands. Can you save by using public transit to get to a hotel or to a rental-car agency further from the airport, where rates are lower? If you need lodging, websites like Quikbook or Hotels.com can help you shop around.