For Champy:

EPA.GOV

Biodiesel (B100)

            Carbon Monoxide -50%

          Particulates -70%

          Total Hydrocarbons – 40%

          Sulfates -100%

          Nitrogen Oxide +9%

          Methane +/- 0%

Ethanol (Grain-E85)

            Carbon Monoxide -40%

          Particulates -20%

          Hydrocarbons –(lower reactivity)

          Sulfates -80%

          Nitrogen Oxide -10%

          Ethanol ++

          Acetaldehyde ++

Compressed Natural Gas

            Carbon Monoxide – 95%

          Carbon Dioxide -25%

          Particulates –little to none

          Hydrocarbons –potential 50-75%

          Sulfates -?

          Nitrogen Oxide -35-60%

          Methane +/- 0%

To put things into perspective,

"Methane traps over 21 times more heat per molecule than carbon dioxide, and nitrous oxide absorbs 270 times more heat per molecule than carbon dioxide."

While I couldn't find detailed emissions information for ethanol based on feedstock it’s important to know that using cellulosic material (whole plants or trees) instead of grains (corn kernels) suggests a reduction of green house gases (methane, CO2 NOx) by up to 80%. But as I said, there is little information on the exact percentages of each.

Comparing Biodiesel and Ethanol can get a bit tricky because some sources argue that Biodiesel results are skewed because the systems use filters and catalysts that aren't used with other alternatives and that it effects emissions, especially particulates greatly. They contend that Filters and CATs are only relevant when in working order and as we've seen in the past are seldom replaced. I for one don't tend to trust the general public to maintain their vehicles in that way as I am guilty myself of ignoring or even hiding a few dead CATs when inspection time came.  Some sites also suggest that diesel engines do not produce the same results in real world conditions as they do in the lab and this again could tie back to the maintenance issue. Realistically we shouldn't be comparing entire systems for this very reason anyway.

It’s going to kill me to say this but for once it looks like my father was right, Compressed Natural Gas seems the way to go from a conservationist’s perspective.  There are however, two drawbacks to CNG that I can point out right away. CNG would require either a new vehicle or a vehicle conversion kit ($4k-5k) which is not necessary with Ethanol or Biodiesel. Conversion on a grand scale would most definitely be costly. My other problem with CNG is that even though it’s in great supply, we're still trading one non-renewable resource for another. Remember, there was a time when Oil was cheap and plentiful.  I have read that biomass can be converted through gasification, but into what I do not know.  If it is indeed methane that would certainly solve the sourcing problem and I know of a certain local college that farms trees for this very process. Unfortunately again, it’s likely the process is too complicated or too expensive to do privately. 

Personally I like hydrogen systems and I know they are testing them in DC but I’m afraid they are probably the furthest away from realization.  Electrical systems are intriguing but until they solve the storage problem they just aren't practical and replacing a battery at least once during the life of the car... are you kidding???  When you consider too the source of the electricity to charge the vehicle and the increase in production on that front electric cars may not be as green as they seem. 

The more I research Alternative Fuels the more I realize that it really is a problem of circles.

Energystar.Gov

If every household in the U.S. replaced one light bulb with an ENERGY STAR qualified compact fluorescent light bulb (CFL), it would prevent enough pollution to equal removing one million cars from the road.

On the other hand, maybe we're just thinking too BIG: