Howdy,
The subject of biodiesel has been discussed to death over on the Volkswagen TDI forum. The main danger centers around the fact that biodiesel is very hygroscopic and can contain water. This can corrode you fuel system, but properly made and stored biodiesel shouldn't have water in it.
The other issue that is discussed alot is that biodiesel is a powerful fuel system cleaner. This is good obviously in that it keeps your injectors clean but does knock loose alot of junk when you switch over. There are some other differences such as higher cetane, better lubricity, much worse cloud point, lower energy content, and no sulfur that are discussed.
Check out the TDI site at:
http://forums.tdiclub.com/NonCGI/ultimatebb.php?category=3
Sholin