(continued ...) For the wide array of combustible hydrocarbons, such as corn, manure, wood pellets, split cord wood and similar, they are also combined with combustion air and an ignition source to create combustion. This releases the stored chemical energy of these products. Again, the heat we want but the byproducts we do not.
The problem with combustion is almost universal. The byproducts are chemically undesirable green house gases and other foul items. On top of that, common heat exchangers cannot extract all the available heat released by the combustion process. The 'benefit' of combustible commodities is that they are generally readily available and cheap compared to other options. This has propagated to readily available and cheap systems, equipment and methods to use those sources. Today, someone on minimum wage in America could afford to buy and install a simple furnace for two month's wages. Until alternative system costs can catch up with (drop down to) combustible fuel systems, many people will likely continue to choose the more economical source of heat: fossil fuels and combustible hydrocarbons.
There is a light at the end of this tunnel. Alternative energy systems are making progress toward better and cheaper. However, it appears to be many years until those options are a clear economical solution. Until then, your choices today are standard energy efficient and high energy efficient versions of combustible fuel furnaces and boilers. Standard energy efficient fossil fuel equipment is about 80% (when properly tuned). That means that the balance of combustion heat goes up your flue or chimney.