There are only 3 drawbacks to using biodiesel as I see it. It doesn't perform as well in cold weather, it eats away at rubber, and it's expensive. Fortunately, most modern engines don't have any rubber in the fuel system.

I think all the positives outweigh the negatives. It's good for the environment, it has the same amount of energy as #2 diesel (if you get good stuff), and it lubricates better than #2 diesel.

I plan on making my own biodiesel in the near future and have been doing a bit of research myself. One thing that I've heard is that once you make the transition to biodiesel, especially on an older engine, you'll have to change the fuel filter quite frequently at first. Apparently it cleans out old crud and deposits form the fuel system and it ends up in the fuel bowl.