If you're considering mid-size cars available in US market, a straightforward comparison would be Prius vs Jetta TDI. The fuel economy of the two is comparable: 49mpg Jetta to 55mpg Prius.
The tailpipe emissions for the Prius are cleaner, but using biodiesel instead of diesel fuel reduces those emissions to a significant degree:
http://www.epa.gov/OMS/models/analysis/biodsl/p02001.pdf
The anticipated longevity of the battery packs for the Prius is a point of contention, and even if they are replaced, that produces heavy metal waste of dead batteries to be disposed of:
http://www.greenhybrid.com/discuss/will-the-battery-of-the-prius-i-last-the-lifetime.534.html
It is clear, however, that the lifetime of the car is claimed to be 100k-200k miles for the Prius, whereas the Jetta TDI very commonly lasts 300k-400k miles. Given the tremendous resources consumed in the manufacture of any new vehicle, the vastly greater durability of a diesel far outweighs the slightly lesser fuel economy.
The better question here should be "Which is more environmentally friendly, two hybrids one after another or a single diesel?"
In Summary: the more ecologically responsible _and_ economically feasable choice is a diesel. (And it's even clearer win for diesel if you're powered by biodiesel or vegetable oil)