I've been reading a lot about biodiesel recently, mainly online, and I have to say it looks like a pretty good fuel. Perhaps even better than H2 fuel cells. By 'better' I mean essentially as clean and similar or increased fuel efficiency (with production taken into account).
It is much cleaner than petrodiesel when burnt (
http://www.journeytoforever.org/biodiesel.html). Even the slight increase in NOx emissions could be reversed by an exhaust technology that can't currently be used because of the sulfur in petrodiesel (
http://www.journeytoforever.org/biodiesel_nox.html). Most importantly, in many environmentalists' minds is that biodiesel is mostly (80-90%) composed of vegetable oil, so it is a carbon neutral fuel, not adding any net CO2 to the atmosphere. So if you're concerned humans cause global warming, this product will at least help level off the CO2 in the atmosphere.
Biodiesel is also better for your engine. It is an incredible solvent (can even strip paint).
It is biodegradeable and non-toxic.
It can be (and it currently) produced using domestically grown veg oil. Therefore no money going to the middle east or big oil companies (for now).
It smells nice when burnt (like donuts).
Engine performance is 'about the same'. I've read about both slight improvements and reductions in power and mileage.
You can even make the stuff your self, and very cheaply. Biodiesel is simply vegetable oil that has had the glycerin removed (through esterification). That process involves mixing about 200ml methonal and a couple grams of lye with a gallon of veg oil and letting it sit for a few hours. You can even use waste veg oil (or WVO, free from restaurants) to make it. (There are other methods of esterification, but that's the one most homebrewers use).
The John Deere article looks to me to be mostly to cover their butts out of liability. Any diesel engine is able to use biodiesel. I do not use biodiesel (have to diesel engines in my possession) and most of the reading I've done has concerned passenger vehicle and pickup trucks. But I've seen articles about it's use in boats, furnaces, and farm equipment. And there's no theoretical reason it should work any worse in those situations. Two problems Deere mentions are definitely possible:
1. Because of biodiesel's superior solvency, it can deteriorate hoses and seals made out of old rubber. The material such car parts are made out of today do not deteriorate via biodiesel and if you've got old rubber it is supposedly cheaply replaced.
2. When a vehicle has been running petrodiesel for a long time (say, 100k miles in a car) it can collect gunk at the bottom of the fuel tank and in the lines, etc. If a biodiesel is used in that vehicle straight (that is, 100% biodiesel. it is often blended to 20%bio/80%petro or less) the solvency of biodiesel can easily pull the petrogunk off the fuel tank which can then get pulled into the fuel lines. This appears to be a common problem in cars, so when switching fuel it is advised that you have a couple extra fuel filters on hand. So this is a temporary problem that can crop up when using B100.
Another of Deere's concerns is kind of possible. Diesel engines were originally designed to burn straight peanut oil, not even biodiesel. And, in fact, they still can. The trouble with straight veg oil (SVO) is that it is much more viscous than petrodiesel so it can coke up fuel injectors. Synthesizing veg oil into biodiesel (removing the glycerine) is one way to make it less viscous, enough so that it runs fine through the engine. But another way is to simply heat the SVO before it goes into the engine. If you heat it to about 170F, the SVO's viscosity is adequately reduced to burn happily in the engine. To accomplish this many people add a second fuel tank to their vehicle that has a little heater in it. Start the car with petrodiesel, after a couple minutes you switch to SVO once it's warm enough. People sell kits to convert a diesel car like this for $500 (
http://www.greasel.com/). Then you can go get some free waste veg oil, filter it, and throw it in your car.
So when Deere mentioned the coking, they may have been thinking of the SVO issue. It may be possible for biodiesel to have similar problems in cold, <40F, weather, but if that's the case it can be blended down slightly (say 20% petrodiesel) to end that problem.
Personally, I'm more excited about the idea of running an SVO car than biodiesel, but I'm not sure if SVO is quite as clean as biodiesel. I'm hoping to get an old diesel car in the next year and start.
Here are some excellent biodiesel websites, they discuss SVO a little, too:
http://www.journeytoforever.org/biodiesel.html
www.biodiesel.org (industry trade group)
http://www.biodieselnow.com/ this site has a big forum with lots of people who run biodiesel in their cars all the time.