Every year (since the mid-1990s) greenercars.org publishes the cleanest cars based on a factory-to-junkyard analysis. I went through the list and picked-out some of the more-interesting cars. The ones that surprised me I put in bold:
http://greenercars.org/highlights_greenest.htm
100 maximum score
59 SmartForTwo EV
58 Spark EV
57 Prius City
55 Leaf EV. Prius, Civic, and other compact hybrids.
54 Mirage, Fiesta (normal nonhybrids) (3 cylinders)(and cleanest manual shift cars)
54 Civic Natural Gas
52 Prius V
50 CRZ (manual hybrid)
46 Jetta TDI (diesel; cleaner than the gasoline version)
40 Ford Transit (van)
37 Tesla Model S EV (dirtier than a diesel)
37 Tacoma (pickup)
36 Odyssey (minivan)
WORST:
21 Bentley Musanne (luxury sedan)
19 Bugatti Veyron (16 cylinder sportscar)