"More and more alternative to the traditional gasoline engine are arriving almost daily. But, for consumers, more options don't make the choice any easier. Hybrid, flex-fuel, diesel - which is best on the wallet, and on the environment?"

http://www.mpt.org/motorweek/autoworld.shtml

They compared a Bluetec Benz to its equivalent, Hybrid Civic to its equivalent, and the Hybrid Tahoe with its equivalent (running both normal gas and E85). I thought it was quite even handed (I watched the show which seems to have more information than the article). Also they tried to match the equivalent trim levels (on the Civic they used the EX trim to compare with the hybrid, and added equipment to the FFV Tahoe to match the hybrid.)

Interestingly they got 48mpg combined for the Civic hybrid so they weren't lead footing all the cars around. Also they article gives cost per mile calculations and I found the below interesting for the Tahoe:

"In terms of fuel-cost-per-mile, the Hybrid leads with a figure of 18.3 cents, followed by the gasoline FFV at 22.9 cents and trailed by the E85 at 27.7 cents per mile."