I'm no HVAC expert, but theoretically it's all about btu's, right? You need to input a certain amount of heat to acheive your goal (choose 250,000btu for example). You can do that by running a 500,000btu/hr boiler for 50% of the time or a 250,000btu/hr boiler continuously. Both situations should use the exact same quanity of fuel. However, there are some issues involving warm up and cool down; and if it didn't save some money, they wouldn't make staged boiler systems with modulating valves. So, just guessing, I'd say you are better off with a "throttled down flame" that only produces the btu's you actually need.
Similarly, they say to size an A/C so that it runs continuously at maximum load. I think that may have something to do with moisture removal though. Sporadic cycling of a boiler could produce excess condensation in the vent and allow for corrosion of the burner.