lowest cost of ownership is in a car that is paid for. Even with very poor mpg, not having the car payment more than makes up for it. It also means you aren't using the resources to manufacture a new car, have it shipped, etc.
To CCrew's point - i read somewhere last year that the environmental impact of a Prius is higher than a traditional car. The manufacturing process of the batteries which use minerals from Canada, shipping the batteries to Japan, then the car back to the US all uses up more than the car saves. And as stated, the research shows the payout isn't there unless you are going to keep the car a long time, which most people don't do.
E85 is inefficient, unless your vehicle is pure e85. the flex fuel set up causes a higher cost per mile when using e85 ( i have a flex fuel and lose 25% mpg when using e85)
I wish I could bike to work. Is 25 miles across a big city with no bike lanes to speak of. My Tundra serves my camping/towing and bike hauling needs well, and will last long beyond the payments.