re: net pollution of plug-in hybrid vs. hybrid vs. conventional, see the following on Calcars:
http://www.calcars.org/vehicles.html#2 Even on a coal based grid, PHEV's are cleaner, and as stated above, the thought is that you can control the pollution much more easily at a central power plant than you can on millions of vehicles. Also, electricity is much more efficient.

As to biodiesel CO2 emissions, I agree that we don't want to encourage the destruction of rain forests to grow palm oil, (the sugar cane referenced in the story isn't used for biodiesel, just ethanol). The bio I purchase currently in the U.S., (perhaps 14 tankfuls in a year), comes from Soybeans grown in the Midwest. Growing them consumes CO2, so relative to producing diesel from petroleum, (so called dino-diesel), I understand that it's more or less neutral with regard to adding CO2 to the atmosphere. As to vehicles I'd rather not be stuck behind, I'd place dino-diesel burning trucks and cars much higher on that list than the same burning bio. With bio, once the vehicle is warmed up, I don't notice any smell at all.

As to electric vehicles not having sufficient range for your occasional long distance trip, that of course is the argument for PHEVs. Run on pure electric most of the time, but have the ability to run as a regular hybrid when you need to. You've probably heard all of this, but if not, please see http://www.calcars.org