Apparently, everything started with a Dust to Dust comparison of the total energy costs of various cars over their entire life-cycle. (Note that their 450+ page paper isn't really a study or research paper. It's more of the sort of presentation you might find in a sales pitch or marketing meeting. So take it as such.) Their conclusion, which is based on a lot of seemingly thorough number crunching but no actual scientific measurements, states that hybrid cars are actually relatively expensive in terms of energy cost per mile compared to some conventional combustion engine cars.

A quick Google search for the other side of the coin will find a fairly balanced exploration into those claims in Prius Versus HUMMER: Exploding the Myth. One of the biggest counter arguments is the CNW claim of a Hummer lasting 35 years and Prius only 10 years. The Pacific Institute takes another look at the CNW report in their Hummer versus Prius:
"Dust to Dust" Report Misleads the Media and Public with Bad Science. Although they don't provide evidence to the contrary, the Pacific Institute does illustrate a lot of reasons why you cannot trust the Dust to Dust report in their reanalysis.

I also mentioned to my coworker my desire to run our next car on biodiesel, and to make our own gas. This would give me better mileage, save money, and have a better impact on the environment. Those are my operating assumptions, of course, based on what I've read. But he responded by stating even biodiesel's soot (i.e. carbon emissions) would be extremely high, and result in a bigger environmental impact than unleaded gasoline.

So I did some more digging and found A Comprehensive Analysis of Biodiesel Impacts on Exhaust Emissions published by the EPA back in 2002. The study only included heavy-duty engines, which I'm guessing are those of 18-wheelers and their ilk, but the basic conclusion is overall emissions are radically reduced in proportion to the percentage of biodiesel in the fuel, except for NO_x which increased slightly in proportion. Overall CO₂ emissions remain about the same, but CO emissions do decrease.

I do need to find some hard numbers for comparision against regular unleaded fuel emissions, but this information at least is very promising. Especially when you consider the advances in engine and exhaust technology that would still apply to diesel engines (sort of) that were more recently manufactured.

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